# This file is the result of combining several RDB files, specifically # T0341.t06.dssp-ebghstl.rdb (weight 1.53986) # T0341.t06.stride-ebghtl.rdb (weight 1.24869) # T0341.t06.str2.rdb (weight 1.54758) # T0341.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 T0341.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0341 # 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 T0341.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 4797 # # ============================================ # Comments from T0341.t06.stride-ebghtl.rdb # ============================================ # TARGET T0341 # Using neural net t06-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 T0341.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 4797 # # ============================================ # Comments from T0341.t06.str2.rdb # ============================================ # TARGET T0341 # 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 T0341.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 4797 # # ============================================ # Comments from T0341.t06.alpha.rdb # ============================================ # TARGET T0341 # Using neural net t06-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 T0341.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 4797 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0392 0.1329 0.8279 2 A 0.0464 0.3528 0.6009 3 A 0.0412 0.4034 0.5553 4 R 0.0509 0.4241 0.5250 5 R 0.0679 0.3103 0.6219 6 A 0.1193 0.1049 0.7758 7 L 0.2063 0.0112 0.7825 8 K 0.2985 0.0351 0.6664 9 A 0.9190 0.0038 0.0772 10 V 0.9328 0.0032 0.0639 11 L 0.9326 0.0032 0.0643 12 V 0.9163 0.0045 0.0792 13 D 0.6998 0.0059 0.2943 14 L 0.2435 0.0732 0.6833 15 N 0.0899 0.0518 0.8583 16 G 0.0922 0.0668 0.8410 17 T 0.3179 0.0929 0.5892 18 L 0.6270 0.0825 0.2905 19 H 0.6027 0.0743 0.3231 20 I 0.3964 0.0770 0.5265 21 E 0.1323 0.1521 0.7156 22 D 0.0805 0.2660 0.6535 23 A 0.0511 0.3239 0.6250 24 A 0.0572 0.2936 0.6492 25 V 0.0524 0.2641 0.6835 26 P 0.0096 0.7921 0.1982 27 G 0.0115 0.8381 0.1504 28 A 0.0053 0.9292 0.0655 29 Q 0.0047 0.9542 0.0411 30 E 0.0047 0.9564 0.0389 31 A 0.0047 0.9583 0.0371 32 L 0.0047 0.9597 0.0356 33 K 0.0047 0.9598 0.0355 34 R 0.0047 0.9591 0.0362 35 L 0.0048 0.9560 0.0392 36 R 0.0049 0.9478 0.0474 37 A 0.0059 0.8896 0.1044 38 T 0.0456 0.3544 0.6000 39 S 0.0505 0.0154 0.9341 40 V 0.1408 0.0099 0.8493 41 M 0.6355 0.0076 0.3569 42 V 0.8681 0.0053 0.1266 43 R 0.8745 0.0092 0.1163 44 F 0.8269 0.0154 0.1577 45 V 0.5718 0.0330 0.3952 46 T 0.2332 0.0478 0.7190 47 N 0.0754 0.0770 0.8476 48 T 0.0762 0.0660 0.8578 49 T 0.0787 0.1028 0.8185 50 K 0.0544 0.2818 0.6638 51 E 0.0662 0.3443 0.5895 52 T 0.0642 0.3594 0.5764 53 K 0.0070 0.9113 0.0817 54 K 0.0053 0.9468 0.0479 55 D 0.0048 0.9517 0.0435 56 L 0.0048 0.9545 0.0408 57 L 0.0047 0.9562 0.0391 58 E 0.0048 0.9528 0.0424 59 R 0.0050 0.9403 0.0547 60 L 0.0079 0.9049 0.0872 61 K 0.0097 0.7751 0.2152 62 K 0.0186 0.6264 0.3550 63 L 0.0728 0.4043 0.5229 64 E 0.1057 0.1961 0.6982 65 F 0.2260 0.1107 0.6632 66 E 0.4510 0.0889 0.4601 67 I 0.4747 0.0652 0.4601 68 S 0.2216 0.0515 0.7269 69 E 0.0695 0.2604 0.6700 70 D 0.0512 0.1679 0.7809 71 E 0.1218 0.1919 0.6862 72 I 0.3261 0.2178 0.4561 73 F 0.4453 0.2538 0.3009 74 T 0.3211 0.2595 0.4194 75 S 0.2185 0.2964 0.4851 76 L 0.0624 0.6680 0.2696 77 T 0.0207 0.8670 0.1123 78 A 0.0202 0.8904 0.0894 79 A 0.0128 0.9171 0.0700 80 R 0.0107 0.9284 0.0609 81 N 0.0095 0.9190 0.0715 82 L 0.0077 0.9125 0.0799 83 I 0.0142 0.8883 0.0975 84 E 0.0141 0.8471 0.1387 85 Q 0.0180 0.7684 0.2136 86 K 0.0444 0.6119 0.3437 87 Q 0.0542 0.3405 0.6053 88 V 0.0801 0.2380 0.6819 89 R 0.0943 0.1815 0.7242 90 P 0.0912 0.4100 0.4988 91 M 0.1378 0.5122 0.3500 92 L 0.2287 0.4334 0.3379 93 L 0.2276 0.3951 0.3773 94 L 0.1368 0.3572 0.5060 95 D 0.0795 0.3141 0.6064 96 D 0.0152 0.6643 0.3205 97 R 0.0169 0.6591 0.3240 98 A 0.0240 0.7000 0.2760 99 L 0.0295 0.6717 0.2988 100 P 0.0133 0.8134 0.1733 101 E 0.0197 0.8128 0.1675 102 F 0.0449 0.7568 0.1983 103 T 0.0485 0.6696 0.2819 104 G 0.0482 0.5673 0.3845 105 V 0.0759 0.4986 0.4255 106 Q 0.1010 0.3314 0.5676 107 T 0.0967 0.2087 0.6946 108 Q 0.0837 0.1311 0.7852 109 D 0.1068 0.0323 0.8610 110 P 0.0197 0.4963 0.4840 111 N 0.0388 0.5487 0.4125 112 A 0.1240 0.5765 0.2995 113 V 0.2583 0.4860 0.2557 114 V 0.3471 0.4193 0.2336 115 I 0.2636 0.3812 0.3551 116 G 0.1687 0.2461 0.5852 117 L 0.1520 0.2085 0.6396 118 A 0.1110 0.1408 0.7482 119 P 0.0416 0.2936 0.6648 120 E 0.0562 0.3957 0.5481 121 H 0.1029 0.3889 0.5082 122 F 0.1247 0.3297 0.5456 123 H 0.1034 0.3342 0.5624 124 Y 0.0447 0.5454 0.4099 125 Q 0.0104 0.8165 0.1731 126 L 0.0097 0.8451 0.1451 127 L 0.0054 0.9286 0.0660 128 N 0.0048 0.9535 0.0417 129 Q 0.0047 0.9574 0.0379 130 A 0.0047 0.9575 0.0378 131 F 0.0048 0.9567 0.0385 132 R 0.0047 0.9542 0.0411 133 L 0.0052 0.9389 0.0559 134 L 0.0061 0.9053 0.0886 135 L 0.0113 0.7981 0.1906 136 D 0.0316 0.3230 0.6454 137 G 0.0294 0.0352 0.9354 138 A 0.0845 0.0113 0.9042 139 P 0.2856 0.0083 0.7061 140 L 0.8483 0.0056 0.1461 141 I 0.8918 0.0051 0.1031 142 A 0.8854 0.0050 0.1096 143 I 0.6864 0.0209 0.2927 144 H 0.2145 0.0296 0.7559 145 K 0.0827 0.1407 0.7766 146 A 0.0674 0.3710 0.5616 147 R 0.0469 0.6803 0.2728 148 Y 0.0497 0.7590 0.1913 149 Y 0.0598 0.7537 0.1866 150 K 0.0694 0.7273 0.2033 151 R 0.0660 0.6918 0.2422 152 K 0.0416 0.7383 0.2202 153 D 0.0324 0.7333 0.2343 154 G 0.0270 0.7293 0.2437 155 L 0.0248 0.6935 0.2818 156 A 0.0297 0.6077 0.3626 157 L 0.0652 0.2856 0.6492 158 G 0.0528 0.0484 0.8987 159 P 0.0593 0.0978 0.8428 160 G 0.0536 0.1784 0.7679 161 P 0.0591 0.3488 0.5921 162 F 0.1286 0.3956 0.4758 163 V 0.3645 0.2470 0.3885 164 T 0.4058 0.2847 0.3095 165 A 0.6524 0.2042 0.1434 166 L 0.7342 0.1554 0.1104 167 E 0.7221 0.1543 0.1236 168 Y 0.5851 0.1262 0.2886 169 A 0.2716 0.0862 0.6422 170 T 0.1552 0.1492 0.6955 171 D 0.1601 0.1407 0.6992 172 T 0.2261 0.2275 0.5463 173 K 0.2670 0.2328 0.5002 174 A 0.3851 0.2434 0.3715 175 M 0.3507 0.2192 0.4301 176 V 0.3290 0.1873 0.4837 177 V 0.1587 0.1545 0.6868 178 G 0.0785 0.0639 0.8576 179 K 0.0713 0.0401 0.8886 180 P 0.0778 0.0693 0.8529 181 E 0.0569 0.1705 0.7726 182 K 0.0091 0.8799 0.1110 183 T 0.0064 0.9290 0.0646 184 F 0.0048 0.9511 0.0441 185 F 0.0047 0.9584 0.0370 186 L 0.0047 0.9604 0.0349 187 E 0.0047 0.9605 0.0348 188 A 0.0047 0.9607 0.0346 189 L 0.0047 0.9590 0.0363 190 R 0.0049 0.9470 0.0481 191 D 0.0058 0.8865 0.1078 192 A 0.0461 0.3749 0.5791 193 D 0.0455 0.0157 0.9388 194 C 0.0660 0.0084 0.9256 195 A 0.0731 0.0107 0.9162 196 P 0.0340 0.6211 0.3448 197 E 0.0494 0.6185 0.3321 198 E 0.1497 0.5058 0.3445 199 A 0.8283 0.0204 0.1513 200 V 0.9001 0.0088 0.0912 201 M 0.9095 0.0067 0.0838 202 I 0.7969 0.0458 0.1573 203 G 0.5088 0.0205 0.4707 204 D 0.2264 0.0423 0.7313 205 D 0.1113 0.0707 0.8181 206 C 0.0524 0.2101 0.7375 207 R 0.0375 0.3815 0.5810 208 D 0.0469 0.3783 0.5748 209 D 0.0602 0.5962 0.3436 210 V 0.0086 0.9206 0.0709 211 D 0.0059 0.9402 0.0539 212 G 0.0048 0.9512 0.0440 213 A 0.0049 0.9519 0.0432 214 Q 0.0050 0.9414 0.0536 215 N 0.0058 0.8942 0.1000 216 I 0.0461 0.4119 0.5420 217 G 0.0378 0.0220 0.9402 218 M 0.1186 0.0084 0.8729 219 L 0.4203 0.0172 0.5624 220 G 0.8763 0.0052 0.1185 221 I 0.9160 0.0045 0.0795 222 L 0.9151 0.0061 0.0788 223 V 0.8366 0.0132 0.1502 224 K 0.5385 0.0291 0.4324 225 T 0.2103 0.0712 0.7184 226 G 0.1275 0.0989 0.7735 227 K 0.2467 0.1485 0.6049 228 Y 0.3112 0.1649 0.5239 229 K 0.2345 0.1989 0.5666 230 A 0.1285 0.3984 0.4732 231 A 0.0873 0.3773 0.5354 232 D 0.0703 0.4179 0.5118 233 E 0.0498 0.6033 0.3470 234 E 0.0450 0.5984 0.3566 235 K 0.0494 0.4986 0.4520 236 I 0.0973 0.2133 0.6895 237 N 0.0624 0.0409 0.8967 238 P 0.0606 0.0232 0.9161 239 P 0.0868 0.0218 0.8913 240 P 0.1729 0.0391 0.7880 241 Y 0.4207 0.0672 0.5120 242 L 0.8197 0.0272 0.1532 243 T 0.8521 0.0237 0.1242 244 C 0.7024 0.0254 0.2722 245 E 0.2730 0.0755 0.6515 246 S 0.1021 0.0427 0.8552 247 F 0.0253 0.5912 0.3835 248 P 0.0057 0.8674 0.1268 249 H 0.0062 0.9014 0.0924 250 A 0.0052 0.9332 0.0616 251 V 0.0048 0.9507 0.0445 252 D 0.0047 0.9547 0.0406 253 H 0.0048 0.9536 0.0416 254 I 0.0048 0.9486 0.0466 255 L 0.0051 0.9402 0.0548 256 Q 0.0070 0.8964 0.0966 257 H 0.0133 0.7735 0.2133 258 L 0.0262 0.5078 0.4660 259 L 0.0319 0.0820 0.8861