# This file is the result of combining several RDB files, specifically # T0238.t04.dssp-ebghstl.rdb (weight 1.53986) # T0238.t04.stride-ebghtl.rdb (weight 1.24869) # T0238.t04.str2.rdb (weight 1.54758) # T0238.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 T0238.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0238 # 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 T0238.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 15 # # ============================================ # Comments from T0238.t04.stride-ebghtl.rdb # ============================================ # TARGET T0238 # 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 T0238.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 15 # # ============================================ # Comments from T0238.t04.str2.rdb # ============================================ # TARGET T0238 # 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 T0238.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 15 # # ============================================ # Comments from T0238.t04.alpha.rdb # ============================================ # TARGET T0238 # 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 T0238.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 15 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0623 0.3154 0.6223 2 K 0.0825 0.4005 0.5170 3 K 0.0904 0.3253 0.5843 4 A 0.2071 0.1698 0.6232 5 K 0.3423 0.1438 0.5140 6 L 0.4578 0.0954 0.4468 7 N 0.3630 0.1489 0.4881 8 I 0.5210 0.2117 0.2673 9 I 0.6054 0.1549 0.2397 10 K 0.5779 0.1669 0.2552 11 I 0.4595 0.1549 0.3856 12 N 0.3433 0.1846 0.4720 13 I 0.2964 0.4975 0.2061 14 I 0.3600 0.4908 0.1492 15 A 0.4460 0.4535 0.1005 16 M 0.4943 0.4226 0.0831 17 I 0.5448 0.3539 0.1014 18 L 0.5540 0.2925 0.1535 19 T 0.5277 0.2479 0.2245 20 L 0.4105 0.2912 0.2983 21 I 0.4124 0.2748 0.3128 22 C 0.5018 0.2267 0.2715 23 T 0.4886 0.1577 0.3537 24 S 0.4430 0.0932 0.4638 25 C 0.2980 0.1021 0.6000 26 A 0.1603 0.1118 0.7279 27 P 0.1097 0.2470 0.6433 28 F 0.0958 0.2280 0.6762 29 S 0.1323 0.1196 0.7481 30 K 0.1346 0.0998 0.7656 31 I 0.1947 0.0649 0.7405 32 D 0.1047 0.0218 0.8735 33 P 0.0122 0.4650 0.5228 34 K 0.0167 0.4687 0.5146 35 A 0.0365 0.5478 0.4158 36 N 0.0595 0.3579 0.5825 37 A 0.0655 0.2812 0.6533 38 N 0.0844 0.0977 0.8179 39 T 0.0885 0.0715 0.8400 40 K 0.1184 0.0284 0.8532 41 P 0.1544 0.0577 0.7880 42 K 0.2254 0.0832 0.6914 43 K 0.3840 0.0564 0.5597 44 I 0.3695 0.0364 0.5942 45 T 0.2949 0.0389 0.6662 46 N 0.1478 0.0167 0.8355 47 P 0.0616 0.0806 0.8578 48 G 0.0764 0.0628 0.8609 49 E 0.1501 0.0899 0.7600 50 N 0.1683 0.0649 0.7668 51 T 0.2146 0.0667 0.7186 52 Q 0.2209 0.0809 0.6981 53 N 0.2535 0.0457 0.7008 54 F 0.1971 0.0957 0.7072 55 E 0.2240 0.0967 0.6793 56 D 0.1375 0.0564 0.8062 57 K 0.0541 0.1356 0.8102 58 S 0.1112 0.0568 0.8320 59 G 0.0950 0.0640 0.8409 60 D 0.1431 0.0311 0.8258 61 L 0.2269 0.1052 0.6679 62 S 0.1044 0.1143 0.7813 63 T 0.0760 0.1100 0.8140 64 S 0.0364 0.1739 0.7897 65 D 0.0474 0.1798 0.7727 66 E 0.0817 0.4734 0.4450 67 K 0.1050 0.5919 0.3030 68 I 0.0741 0.7543 0.1717 69 M 0.0523 0.8265 0.1212 70 E 0.0394 0.8668 0.0938 71 T 0.0304 0.8811 0.0885 72 I 0.0169 0.9026 0.0805 73 A 0.0091 0.9332 0.0577 74 S 0.0057 0.9341 0.0602 75 E 0.0059 0.9190 0.0751 76 L 0.0069 0.9032 0.0899 77 K 0.0059 0.8912 0.1029 78 A 0.0067 0.8424 0.1509 79 I 0.0147 0.7353 0.2500 80 G 0.0214 0.5869 0.3917 81 K 0.0088 0.8072 0.1840 82 E 0.0127 0.8687 0.1187 83 L 0.0091 0.9105 0.0804 84 E 0.0098 0.8777 0.1125 85 D 0.0086 0.8754 0.1160 86 Q 0.0119 0.8013 0.1868 87 K 0.0279 0.7073 0.2647 88 K 0.0625 0.4926 0.4449 89 E 0.0724 0.5024 0.4252 90 E 0.0942 0.4026 0.5032 91 N 0.1004 0.3444 0.5552 92 I 0.1095 0.3359 0.5545 93 Q 0.1705 0.3955 0.4339 94 I 0.1614 0.6336 0.2050 95 A 0.1345 0.6578 0.2077 96 K 0.1449 0.6083 0.2468 97 I 0.1055 0.5591 0.3354 98 A 0.0509 0.6349 0.3142 99 K 0.0164 0.6316 0.3520 100 E 0.0302 0.5461 0.4237 101 K 0.0461 0.5561 0.3978 102 F 0.1235 0.2817 0.5948 103 D 0.1018 0.2832 0.6151 104 F 0.1398 0.4329 0.4273 105 L 0.1766 0.4267 0.3967 106 S 0.2138 0.4460 0.3402 107 T 0.3496 0.3371 0.3133 108 F 0.5582 0.1093 0.3325 109 K 0.5759 0.0300 0.3942 110 V 0.3879 0.0324 0.5797 111 G 0.1398 0.0276 0.8326 112 P 0.1094 0.1938 0.6968 113 Y 0.0852 0.3859 0.5289 114 D 0.1134 0.3658 0.5208 115 L 0.1571 0.4322 0.4107 116 I 0.1735 0.3155 0.5110 117 D 0.1027 0.3143 0.5830 118 E 0.0293 0.4956 0.4751 119 D 0.0411 0.4215 0.5374 120 I 0.0514 0.6355 0.3130 121 Q 0.0587 0.6473 0.2940 122 M 0.0428 0.7827 0.1745 123 K 0.0518 0.8004 0.1478 124 I 0.0791 0.7634 0.1575 125 K 0.1039 0.7056 0.1905 126 R 0.2030 0.5846 0.2125 127 T 0.3428 0.5030 0.1543 128 L 0.3966 0.4735 0.1299 129 Y 0.4675 0.3861 0.1465 130 S 0.4164 0.3657 0.2180 131 S 0.3765 0.3058 0.3178 132 L 0.3311 0.1609 0.5081 133 D 0.2185 0.1126 0.6689 134 Y 0.0752 0.3268 0.5981 135 K 0.0589 0.3073 0.6339 136 K 0.0221 0.6947 0.2832 137 E 0.0172 0.7585 0.2243 138 N 0.0147 0.8152 0.1701 139 I 0.0069 0.9190 0.0740 140 E 0.0060 0.9449 0.0491 141 K 0.0055 0.9491 0.0453 142 L 0.0047 0.9542 0.0410 143 K 0.0047 0.9600 0.0353 144 E 0.0046 0.9614 0.0339 145 I 0.0046 0.9608 0.0346 146 L 0.0047 0.9603 0.0350 147 E 0.0047 0.9602 0.0351 148 I 0.0048 0.9559 0.0393 149 L 0.0052 0.9283 0.0665 150 K 0.0088 0.7565 0.2347 151 K 0.0160 0.5382 0.4459 152 N 0.0667 0.2353 0.6980 153 S 0.0179 0.3319 0.6502 154 E 0.0174 0.4387 0.5439 155 H 0.0325 0.5871 0.3803 156 Y 0.0239 0.6950 0.2811 157 N 0.0219 0.7935 0.1846 158 I 0.0111 0.9171 0.0719 159 I 0.0056 0.9488 0.0457 160 G 0.0056 0.9520 0.0425 161 R 0.0055 0.9542 0.0403 162 L 0.0063 0.9507 0.0430 163 I 0.0063 0.9448 0.0489 164 Y 0.0084 0.9270 0.0646 165 H 0.0100 0.9135 0.0765 166 I 0.0073 0.8872 0.1055 167 S 0.0085 0.8714 0.1201 168 W 0.0077 0.9049 0.0874 169 G 0.0076 0.9261 0.0664 170 I 0.0062 0.9411 0.0528 171 Q 0.0057 0.9517 0.0426 172 F 0.0047 0.9573 0.0380 173 Q 0.0047 0.9488 0.0465 174 I 0.0047 0.9479 0.0474 175 E 0.0047 0.9573 0.0380 176 Q 0.0049 0.9517 0.0434 177 N 0.0050 0.9394 0.0555 178 L 0.0048 0.9490 0.0462 179 E 0.0047 0.9483 0.0470 180 L 0.0047 0.9450 0.0502 181 I 0.0058 0.9359 0.0582 182 Q 0.0077 0.8970 0.0954 183 N 0.0169 0.7252 0.2579 184 G 0.0149 0.5275 0.4576 185 V 0.0385 0.5421 0.4194 186 E 0.0313 0.5602 0.4085 187 N 0.0464 0.5495 0.4041 188 L 0.0961 0.2999 0.6040 189 S 0.0738 0.1872 0.7390 190 Q 0.0080 0.8153 0.1767 191 E 0.0057 0.8921 0.1022 192 E 0.0089 0.8702 0.1209 193 S 0.0057 0.9269 0.0674 194 K 0.0047 0.9554 0.0398 195 S 0.0047 0.9564 0.0389 196 L 0.0047 0.9548 0.0405 197 L 0.0048 0.9551 0.0401 198 M 0.0049 0.9435 0.0516 199 Q 0.0054 0.9301 0.0645 200 I 0.0067 0.9224 0.0709 201 K 0.0058 0.9163 0.0779 202 S 0.0131 0.8794 0.1075 203 N 0.0122 0.8563 0.1315 204 L 0.0104 0.9010 0.0886 205 E 0.0111 0.9036 0.0853 206 I 0.0078 0.9422 0.0500 207 K 0.0058 0.9522 0.0421 208 Q 0.0055 0.9557 0.0388 209 R 0.0048 0.9512 0.0439 210 L 0.0049 0.9506 0.0446 211 K 0.0048 0.9571 0.0381 212 K 0.0049 0.9585 0.0367 213 T 0.0048 0.9588 0.0365 214 L 0.0047 0.9605 0.0348 215 N 0.0047 0.9609 0.0344 216 E 0.0047 0.9589 0.0365 217 T 0.0047 0.9554 0.0399 218 L 0.0048 0.9470 0.0483 219 K 0.0057 0.9185 0.0758 220 V 0.0087 0.8806 0.1106 221 Y 0.0283 0.7552 0.2166 222 N 0.0430 0.3324 0.6246 223 Q 0.0224 0.3315 0.6460 224 N 0.0410 0.2059 0.7531 225 T 0.0704 0.1764 0.7532 226 Q 0.0866 0.2601 0.6533 227 D 0.0985 0.3497 0.5518 228 N 0.0618 0.4296 0.5085 229 E 0.0406 0.7118 0.2476 230 K 0.0303 0.8598 0.1099 231 I 0.0344 0.8680 0.0976 232 L 0.0174 0.8840 0.0986 233 A 0.0108 0.9143 0.0749 234 E 0.0063 0.9317 0.0621 235 H 0.0062 0.9354 0.0585 236 F 0.0099 0.9103 0.0799 237 N 0.0118 0.8676 0.1206 238 K 0.0145 0.8227 0.1628 239 Y 0.0219 0.7452 0.2329 240 Y 0.0711 0.5129 0.4160 241 K 0.0517 0.4239 0.5244 242 D 0.0723 0.2747 0.6530 243 F 0.0505 0.4360 0.5135 244 D 0.0361 0.4927 0.4712 245 T 0.0575 0.4769 0.4655 246 L 0.0701 0.4066 0.5233 247 K 0.0617 0.3505 0.5878 248 P 0.0477 0.4753 0.4769 249 A 0.0518 0.3828 0.5654 250 F 0.0643 0.1725 0.7631 251 Y 0.0491 0.0539 0.8970