# This file is the result of combining several RDB files, specifically # T0191.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0191.t2k.stride-ebghtl.rdb (weight 1.24869) # T0191.t2k.str.rdb (weight 1.53983) # T0191.t2k.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 T0191.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0191 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0191.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 175 # # ============================================ # Comments from T0191.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0191 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0191.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 175 # # ============================================ # Comments from T0191.t2k.str.rdb # ============================================ # TARGET T0191 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0191.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 175 # # ============================================ # Comments from T0191.t2k.alpha.rdb # ============================================ # TARGET T0191 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0191.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 175 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0553 0.0325 0.9123 2 I 0.1277 0.0370 0.8353 3 N 0.1232 0.0424 0.8345 4 A 0.1140 0.0742 0.8118 5 K 0.1546 0.0585 0.7869 6 T 0.2840 0.0525 0.6636 7 K 0.5264 0.0393 0.4342 8 V 0.7698 0.0224 0.2078 9 I 0.8374 0.0221 0.1406 10 G 0.8478 0.0205 0.1316 11 L 0.8370 0.0221 0.1410 12 I 0.6132 0.0442 0.3426 13 G 0.2988 0.0342 0.6670 14 H 0.1836 0.0398 0.7766 15 P 0.1526 0.1048 0.7425 16 V 0.1217 0.2567 0.6215 17 E 0.0975 0.2594 0.6431 18 H 0.0870 0.2248 0.6882 19 S 0.0959 0.1353 0.7688 20 F 0.0561 0.1460 0.7978 21 S 0.0523 0.1361 0.8117 22 P 0.0156 0.7577 0.2268 23 I 0.0150 0.8546 0.1305 24 M 0.0125 0.9068 0.0806 25 H 0.0085 0.9279 0.0636 26 N 0.0067 0.9360 0.0573 27 A 0.0053 0.9434 0.0513 28 A 0.0046 0.9479 0.0475 29 F 0.0048 0.9481 0.0471 30 K 0.0056 0.9358 0.0586 31 D 0.0071 0.8887 0.1041 32 K 0.0434 0.4977 0.4589 33 G 0.0450 0.0484 0.9066 34 L 0.0947 0.0283 0.8769 35 N 0.1505 0.0664 0.7831 36 Y 0.4494 0.1062 0.4444 37 V 0.6660 0.0793 0.2548 38 Y 0.7254 0.0703 0.2043 39 V 0.6283 0.0827 0.2891 40 A 0.4591 0.1198 0.4211 41 F 0.3688 0.1456 0.4856 42 D 0.3796 0.1178 0.5026 43 V 0.2386 0.0901 0.6713 44 L 0.1212 0.0630 0.8158 45 P 0.0189 0.6865 0.2946 46 E 0.0073 0.7312 0.2615 47 N 0.0090 0.7951 0.1958 48 L 0.0064 0.9058 0.0878 49 K 0.0045 0.9435 0.0519 50 Y 0.0045 0.9483 0.0472 51 V 0.0045 0.9518 0.0437 52 I 0.0049 0.9496 0.0455 53 D 0.0054 0.9425 0.0521 54 G 0.0058 0.9267 0.0675 55 A 0.0080 0.9070 0.0850 56 K 0.0138 0.8547 0.1314 57 A 0.0308 0.6563 0.3130 58 L 0.0435 0.2441 0.7124 59 G 0.0440 0.0389 0.9170 60 I 0.1794 0.0298 0.7908 61 V 0.2736 0.0519 0.6745 62 G 0.4413 0.0519 0.5068 63 F 0.6597 0.0347 0.3056 64 N 0.7470 0.0238 0.2292 65 V 0.6949 0.0363 0.2688 66 T 0.5380 0.0558 0.4062 67 I 0.3025 0.1523 0.5453 68 P 0.1331 0.3266 0.5403 69 H 0.0944 0.4564 0.4493 70 K 0.0553 0.6932 0.2515 71 I 0.0196 0.8582 0.1222 72 E 0.0165 0.8698 0.1138 73 I 0.0132 0.8686 0.1182 74 M 0.0108 0.8830 0.1063 75 K 0.0079 0.8587 0.1334 76 Y 0.0081 0.8445 0.1474 77 L 0.0162 0.8132 0.1705 78 D 0.0096 0.7437 0.2466 79 E 0.0155 0.5997 0.3848 80 I 0.0492 0.3997 0.5510 81 D 0.0522 0.2880 0.6598 82 K 0.0049 0.9200 0.0751 83 D 0.0047 0.9256 0.0697 84 A 0.0053 0.9257 0.0690 85 Q 0.0075 0.9054 0.0871 86 L 0.0128 0.8408 0.1464 87 I 0.0646 0.4744 0.4610 88 G 0.0853 0.1790 0.7357 89 A 0.2151 0.1687 0.6162 90 V 0.4059 0.1150 0.4791 91 N 0.5008 0.0856 0.4136 92 T 0.7188 0.0369 0.2443 93 I 0.8114 0.0228 0.1658 94 K 0.8365 0.0133 0.1503 95 I 0.5185 0.0245 0.4570 96 E 0.1212 0.1041 0.7747 97 D 0.0594 0.0361 0.9045 98 G 0.1222 0.0548 0.8230 99 K 0.4750 0.0312 0.4938 100 A 0.6836 0.0234 0.2931 101 I 0.5467 0.0441 0.4092 102 G 0.4310 0.0594 0.5096 103 Y 0.2967 0.1525 0.5508 104 N 0.2152 0.2992 0.4856 105 T 0.1358 0.4419 0.4223 106 D 0.0450 0.7411 0.2139 107 G 0.0108 0.9174 0.0718 108 I 0.0058 0.9502 0.0441 109 G 0.0047 0.9561 0.0392 110 A 0.0044 0.9589 0.0367 111 R 0.0044 0.9593 0.0363 112 M 0.0044 0.9565 0.0392 113 A 0.0044 0.9509 0.0447 114 L 0.0045 0.9449 0.0506 115 E 0.0049 0.9196 0.0755 116 E 0.0075 0.8301 0.1625 117 E 0.0365 0.5363 0.4272 118 I 0.0577 0.1339 0.8084 119 G 0.0811 0.0943 0.8246 120 R 0.1152 0.0803 0.8045 121 V 0.0643 0.2789 0.6568 122 K 0.0281 0.2619 0.7100 123 D 0.0421 0.1545 0.8033 124 K 0.2642 0.0214 0.7144 125 N 0.7563 0.0053 0.2383 126 I 0.9256 0.0041 0.0703 127 V 0.9316 0.0036 0.0648 128 I 0.9249 0.0038 0.0713 129 Y 0.7881 0.0276 0.1843 130 G 0.3327 0.0197 0.6476 131 A 0.0597 0.1277 0.8125 132 G 0.0299 0.4536 0.5166 133 G 0.0057 0.9043 0.0899 134 A 0.0045 0.9437 0.0518 135 A 0.0044 0.9550 0.0406 136 R 0.0044 0.9581 0.0375 137 A 0.0044 0.9590 0.0367 138 V 0.0043 0.9592 0.0365 139 A 0.0044 0.9590 0.0366 140 F 0.0044 0.9569 0.0387 141 E 0.0044 0.9542 0.0414 142 L 0.0047 0.9412 0.0541 143 A 0.0051 0.8928 0.1022 144 K 0.0080 0.7257 0.2663 145 D 0.0484 0.3062 0.6455 146 N 0.0441 0.0421 0.9138 147 N 0.1458 0.0313 0.8229 148 I 0.7866 0.0053 0.2081 149 I 0.9036 0.0042 0.0923 150 I 0.9136 0.0041 0.0823 151 A 0.8452 0.0257 0.1291 152 N 0.6591 0.0095 0.3314 153 R 0.1471 0.0449 0.8080 154 T 0.0923 0.0190 0.8887 155 V 0.0055 0.8587 0.1358 156 E 0.0050 0.9192 0.0758 157 K 0.0047 0.9351 0.0602 158 A 0.0044 0.9490 0.0466 159 E 0.0045 0.9487 0.0468 160 A 0.0045 0.9418 0.0538 161 L 0.0045 0.9363 0.0592 162 A 0.0047 0.9306 0.0647 163 K 0.0052 0.8975 0.0973 164 E 0.0067 0.8470 0.1463 165 I 0.0256 0.7153 0.2591 166 A 0.0178 0.5499 0.4323 167 E 0.0216 0.5167 0.4618 168 K 0.0394 0.4301 0.5305 169 L 0.0602 0.2643 0.6754 170 N 0.0803 0.2371 0.6826 171 K 0.1367 0.2637 0.5996 172 K 0.1773 0.2742 0.5486 173 F 0.2805 0.2126 0.5069 174 G 0.2415 0.1034 0.6551 175 E 0.4169 0.1052 0.4779 176 E 0.4960 0.1129 0.3911 177 V 0.3717 0.0981 0.5302 178 K 0.1941 0.1012 0.7048 179 F 0.0395 0.4776 0.4829 180 S 0.0202 0.5275 0.4523 181 G 0.0244 0.5831 0.3924 182 L 0.0109 0.7673 0.2218 183 D 0.0072 0.8444 0.1483 184 V 0.0069 0.8460 0.1471 185 D 0.0090 0.7995 0.1915 186 L 0.0206 0.7561 0.2233 187 D 0.0149 0.5231 0.4620 188 G 0.0297 0.2540 0.7163 189 V 0.1177 0.0334 0.8489 190 D 0.1221 0.0507 0.8272 191 I 0.9019 0.0046 0.0936 192 I 0.9322 0.0035 0.0643 193 I 0.9277 0.0040 0.0683 194 N 0.8816 0.0065 0.1119 195 A 0.4894 0.0179 0.4928 196 T 0.2444 0.0196 0.7360 197 P 0.1584 0.0538 0.7878 198 I 0.0842 0.1212 0.7945 199 G 0.0650 0.1063 0.8287 200 M 0.0965 0.0824 0.8211 201 Y 0.1451 0.0742 0.7808 202 P 0.1495 0.1031 0.7475 203 N 0.1011 0.0928 0.8061 204 I 0.0530 0.2065 0.7404 205 D 0.0445 0.2040 0.7515 206 V 0.0686 0.2158 0.7156 207 E 0.1005 0.1963 0.7033 208 P 0.1129 0.2118 0.6753 209 I 0.1313 0.3003 0.5684 210 V 0.1178 0.3196 0.5626 211 K 0.0952 0.3420 0.5628 212 A 0.0275 0.7483 0.2242 213 E 0.0295 0.7323 0.2382 214 K 0.0373 0.6688 0.2940 215 L 0.0820 0.4458 0.4723 216 R 0.0708 0.2070 0.7222 217 E 0.0609 0.1131 0.8260 218 D 0.0742 0.0660 0.8598 219 M 0.3036 0.0216 0.6749 220 V 0.8399 0.0052 0.1549 221 V 0.9088 0.0048 0.0864 222 M 0.9039 0.0064 0.0898 223 D 0.8722 0.0103 0.1175 224 L 0.6947 0.0240 0.2813 225 I 0.4549 0.0320 0.5131 226 Y 0.2135 0.0321 0.7544 227 N 0.1127 0.0311 0.8562 228 P 0.0608 0.1189 0.8202 229 L 0.0730 0.1075 0.8195 230 E 0.0512 0.2063 0.7425 231 T 0.0462 0.3617 0.5921 232 V 0.0222 0.7520 0.2259 233 L 0.0150 0.8322 0.1528 234 L 0.0077 0.9101 0.0822 235 K 0.0060 0.9248 0.0692 236 E 0.0050 0.9420 0.0530 237 A 0.0053 0.9401 0.0547 238 K 0.0050 0.9258 0.0692 239 K 0.0060 0.8527 0.1413 240 V 0.0431 0.3759 0.5809 241 N 0.0420 0.0375 0.9204 242 A 0.1653 0.0324 0.8024 243 K 0.6219 0.0403 0.3378 244 T 0.6559 0.0552 0.2889 245 I 0.4500 0.0843 0.4657 246 N 0.1760 0.1249 0.6991 247 G 0.0679 0.3015 0.6306 248 L 0.0564 0.7306 0.2130 249 G 0.0397 0.8208 0.1395 250 M 0.0662 0.8310 0.1028 251 L 0.1022 0.8145 0.0833 252 I 0.0573 0.8783 0.0645 253 Y 0.0307 0.9020 0.0674 254 Q 0.0181 0.9009 0.0810 255 G 0.0118 0.8997 0.0885 256 A 0.0067 0.9229 0.0704 257 V 0.0061 0.9285 0.0653 258 A 0.0056 0.9238 0.0705 259 F 0.0090 0.9226 0.0684 260 K 0.0121 0.9165 0.0714 261 I 0.0129 0.8966 0.0905 262 W 0.0188 0.8290 0.1522 263 T 0.0535 0.5017 0.4448 264 G 0.0422 0.0869 0.8708 265 V 0.0748 0.0427 0.8825 266 E 0.1211 0.0342 0.8447 267 P 0.0835 0.0513 0.8653 268 N 0.0759 0.0764 0.8477 269 I 0.0131 0.8089 0.1780 270 E 0.0077 0.9063 0.0860 271 V 0.0057 0.9339 0.0604 272 M 0.0065 0.9367 0.0568 273 K 0.0057 0.9461 0.0482 274 N 0.0048 0.9499 0.0453 275 A 0.0045 0.9515 0.0441 276 I 0.0045 0.9442 0.0513 277 I 0.0046 0.9347 0.0607 278 D 0.0052 0.9018 0.0930 279 K 0.0076 0.8176 0.1747 280 I 0.0311 0.6296 0.3393 281 T 0.0331 0.4103 0.5566 282 K 0.0244 0.0723 0.9033