# This file is the result of combining several RDB files, specifically # T0381.t06.dssp-ebghstl.rdb (weight 1.53986) # T0381.t06.stride-ebghtl.rdb (weight 1.24869) # T0381.t06.str2.rdb (weight 1.54758) # T0381.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 T0381.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1132 # # ============================================ # Comments from T0381.t06.stride-ebghtl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1132 # # ============================================ # Comments from T0381.t06.str2.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1132 # # ============================================ # Comments from T0381.t06.alpha.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1132 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0675 0.0168 0.9157 2 T 0.0843 0.0307 0.8849 3 A 0.0585 0.1195 0.8221 4 T 0.0679 0.1070 0.8251 5 E 0.0727 0.0742 0.8531 6 P 0.0684 0.1055 0.8262 7 T 0.0727 0.2262 0.7011 8 E 0.0451 0.4568 0.4981 9 K 0.0538 0.4045 0.5417 10 I 0.0896 0.2236 0.6868 11 L 0.0801 0.0510 0.8688 12 P 0.0589 0.0529 0.8882 13 S 0.0759 0.0277 0.8965 14 P 0.0205 0.3681 0.6114 15 D 0.0237 0.4588 0.5176 16 Y 0.0297 0.6801 0.2902 17 V 0.0328 0.7932 0.1739 18 Q 0.0150 0.8729 0.1121 19 S 0.0115 0.9203 0.0682 20 L 0.0048 0.9506 0.0445 21 A 0.0047 0.9565 0.0388 22 R 0.0048 0.9551 0.0401 23 G 0.0047 0.9588 0.0365 24 L 0.0047 0.9593 0.0360 25 A 0.0047 0.9605 0.0348 26 V 0.0047 0.9597 0.0357 27 I 0.0047 0.9580 0.0373 28 R 0.0048 0.9495 0.0457 29 C 0.0053 0.9292 0.0655 30 F 0.0102 0.8453 0.1445 31 D 0.0225 0.6797 0.2978 32 H 0.0220 0.5686 0.4094 33 R 0.0468 0.3714 0.5818 34 N 0.0397 0.1805 0.7798 35 Q 0.0512 0.1309 0.8179 36 R 0.1153 0.0839 0.8008 37 R 0.1851 0.0342 0.7807 38 T 0.1286 0.0223 0.8491 39 L 0.0048 0.9499 0.0453 40 S 0.0047 0.9601 0.0353 41 D 0.0047 0.9597 0.0356 42 V 0.0047 0.9604 0.0349 43 A 0.0047 0.9590 0.0363 44 R 0.0049 0.9430 0.0522 45 A 0.0057 0.8836 0.1107 46 T 0.0467 0.5033 0.4500 47 D 0.0389 0.0734 0.8877 48 L 0.0568 0.0255 0.9177 49 T 0.0569 0.0465 0.8966 50 R 0.0098 0.8208 0.1694 51 A 0.0070 0.9155 0.0774 52 T 0.0051 0.9414 0.0535 53 A 0.0047 0.9586 0.0367 54 R 0.0047 0.9603 0.0350 55 R 0.0046 0.9606 0.0347 56 F 0.0047 0.9603 0.0351 57 L 0.0047 0.9608 0.0345 58 L 0.0047 0.9597 0.0356 59 T 0.0047 0.9602 0.0352 60 L 0.0047 0.9596 0.0358 61 V 0.0048 0.9541 0.0412 62 E 0.0053 0.9212 0.0735 63 L 0.0436 0.4748 0.4816 64 G 0.0293 0.0524 0.9183 65 Y 0.1820 0.0984 0.7196 66 V 0.6964 0.0505 0.2531 67 A 0.7326 0.0295 0.2379 68 T 0.7287 0.0281 0.2432 69 D 0.2972 0.0279 0.6749 70 G 0.0352 0.0726 0.8922 71 S 0.0683 0.0677 0.8641 72 A 0.3931 0.0555 0.5514 73 F 0.6783 0.0193 0.3024 74 W 0.6993 0.0195 0.2812 75 L 0.4461 0.0319 0.5220 76 T 0.1245 0.0472 0.8283 77 P 0.0112 0.9026 0.0861 78 R 0.0081 0.9367 0.0552 79 V 0.0067 0.9504 0.0429 80 L 0.0098 0.9460 0.0441 81 E 0.0089 0.9367 0.0545 82 L 0.0084 0.9024 0.0893 83 G 0.0117 0.8819 0.1063 84 Y 0.0123 0.8880 0.0997 85 S 0.0121 0.8762 0.1117 86 Y 0.0146 0.8422 0.1432 87 L 0.0254 0.7552 0.2194 88 S 0.0156 0.5776 0.4068 89 S 0.0249 0.3929 0.5822 90 L 0.0605 0.1489 0.7906 91 S 0.0686 0.0958 0.8355 92 L 0.0243 0.6012 0.3746 93 P 0.0176 0.8132 0.1692 94 E 0.0119 0.8606 0.1275 95 V 0.0120 0.8280 0.1600 96 A 0.0156 0.7793 0.2051 97 Q 0.0096 0.8670 0.1234 98 P 0.0053 0.9238 0.0709 99 H 0.0049 0.9464 0.0487 100 L 0.0047 0.9549 0.0403 101 E 0.0047 0.9576 0.0377 102 K 0.0047 0.9533 0.0420 103 L 0.0048 0.9480 0.0472 104 S 0.0048 0.9411 0.0540 105 H 0.0052 0.8821 0.1127 106 K 0.0083 0.7534 0.2383 107 V 0.0706 0.3588 0.5706 108 H 0.0616 0.1032 0.8351 109 E 0.1964 0.0747 0.7290 110 S 0.5390 0.0362 0.4248 111 S 0.7449 0.0242 0.2310 112 S 0.8579 0.0141 0.1280 113 V 0.8984 0.0098 0.0918 114 S 0.9118 0.0069 0.0813 115 I 0.9022 0.0063 0.0915 116 L 0.8017 0.0191 0.1792 117 D 0.3831 0.0239 0.5930 118 G 0.0635 0.0451 0.8913 119 A 0.1135 0.0664 0.8201 120 D 0.6445 0.0132 0.3423 121 I 0.9020 0.0033 0.0947 122 V 0.9268 0.0035 0.0696 123 Y 0.9282 0.0036 0.0682 124 V 0.9230 0.0035 0.0735 125 A 0.8813 0.0103 0.1084 126 R 0.8062 0.0080 0.1859 127 V 0.5952 0.0080 0.3968 128 P 0.3687 0.0162 0.6151 129 V 0.1788 0.0653 0.7560 130 S 0.1194 0.1172 0.7635 131 R 0.1981 0.0958 0.7062 132 I 0.4371 0.0535 0.5094 133 M 0.6223 0.0357 0.3420 134 T 0.7428 0.0276 0.2297 135 V 0.6977 0.0366 0.2657 136 G 0.6050 0.0252 0.3699 137 I 0.4441 0.0227 0.5332 138 T 0.3557 0.0258 0.6185 139 I 0.1517 0.1414 0.7069 140 G 0.0935 0.0944 0.8122 141 T 0.2658 0.0819 0.6523 142 R 0.4333 0.0677 0.4990 143 L 0.3097 0.0784 0.6119 144 P 0.1972 0.1519 0.6508 145 A 0.1140 0.4702 0.4159 146 Y 0.1056 0.5335 0.3610 147 A 0.0933 0.5489 0.3579 148 T 0.0563 0.5999 0.3438 149 S 0.0231 0.7868 0.1901 150 M 0.0101 0.8999 0.0899 151 G 0.0083 0.9298 0.0619 152 R 0.0101 0.9445 0.0454 153 V 0.0089 0.9495 0.0415 154 L 0.0096 0.9389 0.0515 155 L 0.0146 0.8691 0.1163 156 A 0.0367 0.6000 0.3633 157 G 0.0306 0.2623 0.7071 158 L 0.0578 0.0147 0.9276 159 P 0.0530 0.0133 0.9337 160 D 0.0054 0.8820 0.1126 161 D 0.0048 0.9390 0.0562 162 E 0.0049 0.9496 0.0455 163 L 0.0048 0.9560 0.0392 164 D 0.0047 0.9560 0.0393 165 A 0.0048 0.9513 0.0439 166 Y 0.0049 0.9444 0.0507 167 L 0.0058 0.9207 0.0735 168 E 0.0059 0.8446 0.1495 169 K 0.0091 0.6314 0.3595 170 L 0.0574 0.3283 0.6142 171 D 0.0782 0.1280 0.7939 172 I 0.0762 0.3388 0.5850 173 Q 0.0873 0.4469 0.4658 174 R 0.1185 0.4538 0.4278 175 L 0.1381 0.2728 0.5891 176 T 0.1181 0.1087 0.7733 177 E 0.0352 0.3198 0.6450 178 R 0.0607 0.2065 0.7328 179 T 0.1226 0.1813 0.6961 180 I 0.1407 0.1514 0.7079 181 T 0.1518 0.0858 0.7623 182 A 0.0896 0.0719 0.8385 183 R 0.0050 0.9399 0.0550 184 D 0.0047 0.9574 0.0380 185 E 0.0047 0.9596 0.0358 186 L 0.0047 0.9590 0.0363 187 K 0.0047 0.9606 0.0348 188 A 0.0047 0.9603 0.0351 189 A 0.0047 0.9588 0.0365 190 I 0.0047 0.9579 0.0374 191 L 0.0047 0.9573 0.0379 192 A 0.0048 0.9541 0.0411 193 V 0.0050 0.9476 0.0473 194 R 0.0063 0.9313 0.0624 195 A 0.0118 0.7868 0.2015 196 D 0.0419 0.2715 0.6866 197 G 0.0534 0.0897 0.8569 198 I 0.2968 0.0786 0.6246 199 C 0.7163 0.0507 0.2331 200 V 0.6834 0.0596 0.2570 201 L 0.5048 0.0721 0.4231 202 D 0.1315 0.3268 0.5417 203 Q 0.0782 0.5058 0.4160 204 E 0.1557 0.5538 0.2906 205 L 0.2030 0.4839 0.3131 206 E 0.1843 0.4346 0.3810 207 A 0.0872 0.3426 0.5701 208 G 0.1331 0.0971 0.7698 209 L 0.4301 0.0352 0.5347 210 R 0.6301 0.0444 0.3255 211 S 0.8795 0.0129 0.1076 212 M 0.9006 0.0082 0.0912 213 A 0.8940 0.0068 0.0993 214 A 0.8351 0.0063 0.1585 215 P 0.7592 0.0079 0.2329 216 I 0.7061 0.0163 0.2775 217 R 0.5595 0.0341 0.4063 218 G 0.1500 0.0418 0.8082 219 A 0.0294 0.1520 0.8186 220 S 0.0509 0.0447 0.9045 221 G 0.0540 0.0323 0.9137 222 L 0.2416 0.0110 0.7474 223 T 0.7944 0.0037 0.2019 224 V 0.8618 0.0145 0.1237 225 A 0.9241 0.0043 0.0716 226 A 0.9306 0.0035 0.0659 227 V 0.9264 0.0042 0.0694 228 N 0.9148 0.0050 0.0802 229 I 0.8406 0.0134 0.1460 230 S 0.6036 0.0309 0.3655 231 T 0.2668 0.0323 0.7010 232 P 0.1551 0.1365 0.7084 233 A 0.0798 0.4296 0.4906 234 A 0.0854 0.4064 0.5082 235 R 0.1355 0.2764 0.5882 236 Y 0.1905 0.0536 0.7559 237 S 0.1165 0.0323 0.8512 238 L 0.0058 0.8946 0.0996 239 E 0.0052 0.9234 0.0714 240 D 0.0051 0.9217 0.0732 241 L 0.0057 0.9168 0.0775 242 H 0.0061 0.9025 0.0914 243 S 0.0064 0.8570 0.1365 244 D 0.0064 0.8271 0.1666 245 L 0.0074 0.8545 0.1381 246 I 0.0053 0.9214 0.0733 247 P 0.0047 0.9550 0.0402 248 S 0.0047 0.9593 0.0360 249 L 0.0047 0.9603 0.0350 250 R 0.0046 0.9612 0.0342 251 V 0.0047 0.9607 0.0347 252 T 0.0047 0.9581 0.0372 253 A 0.0047 0.9578 0.0375 254 T 0.0049 0.9529 0.0422 255 D 0.0049 0.9412 0.0539 256 I 0.0051 0.9309 0.0640 257 E 0.0056 0.9251 0.0693 258 Q 0.0067 0.8956 0.0978 259 D 0.0103 0.8202 0.1695 260 L 0.0376 0.6539 0.3085 261 A 0.0410 0.3611 0.5979 262 T 0.0603 0.2861 0.6536 263 V 0.0789 0.2086 0.7125 264 N 0.0612 0.0676 0.8712 265 R 0.0340 0.0549 0.9111