# This file is the result of combining several RDB files, specifically # T0513.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0513.t2k.stride-ebghtl.rdb (weight 1.24869) # T0513.t2k.str.rdb (weight 1.53983) # 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 T0513.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0513 # 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 T0513.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 146 # # ============================================ # Comments from T0513.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0513 # 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 T0513.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 146 # # ============================================ # Comments from T0513.t2k.str.rdb # ============================================ # TARGET T0513 # 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 T0513.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 146 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0200 0.0194 0.9606 2 S 0.0873 0.1056 0.8071 3 F 0.0729 0.2055 0.7216 4 L 0.0308 0.2783 0.6909 5 K 0.0225 0.3897 0.5877 6 H 0.0188 0.6645 0.3168 7 V 0.0199 0.7814 0.1987 8 Q 0.0190 0.8226 0.1584 9 D 0.0247 0.8037 0.1716 10 C 0.0264 0.7432 0.2304 11 N 0.0286 0.5542 0.4172 12 T 0.0387 0.3703 0.5910 13 H 0.0468 0.1642 0.7890 14 D 0.0373 0.1399 0.8228 15 L 0.0239 0.3686 0.6074 16 S 0.0332 0.3721 0.5947 17 N 0.1181 0.2378 0.6442 18 F 0.3812 0.0690 0.5498 19 V 0.6390 0.0194 0.3416 20 R 0.7704 0.0116 0.2180 21 F 0.8064 0.0091 0.1846 22 V 0.6384 0.0120 0.3497 23 I 0.5585 0.0209 0.4206 24 E 0.0646 0.0259 0.9094 25 G 0.0660 0.0317 0.9023 26 R 0.5689 0.0140 0.4172 27 R 0.7864 0.0076 0.2060 28 V 0.8504 0.0077 0.1419 29 G 0.8369 0.0116 0.1515 30 W 0.8053 0.0140 0.1807 31 V 0.6478 0.0163 0.3359 32 R 0.2253 0.0305 0.7442 33 K 0.0063 0.8165 0.1773 34 A 0.0044 0.8819 0.1138 35 L 0.0046 0.9195 0.0759 36 A 0.0043 0.9281 0.0676 37 Q 0.0050 0.8849 0.1101 38 R 0.0054 0.8572 0.1374 39 L 0.0111 0.7892 0.1997 40 K 0.0175 0.5824 0.4001 41 A 0.0259 0.3763 0.5979 42 H 0.0372 0.1512 0.8116 43 G 0.0417 0.1869 0.7715 44 R 0.0804 0.2086 0.7110 45 V 0.2901 0.1750 0.5349 46 F 0.5372 0.0792 0.3836 47 D 0.6124 0.0454 0.3422 48 V 0.4387 0.0355 0.5258 49 T 0.1784 0.0495 0.7721 50 R 0.0968 0.1537 0.7495 51 D 0.2259 0.1679 0.6063 52 A 0.6005 0.1004 0.2991 53 V 0.7726 0.0539 0.1735 54 L 0.7971 0.0525 0.1504 55 L 0.6867 0.0580 0.2554 56 S 0.3495 0.0560 0.5945 57 A 0.1399 0.1010 0.7591 58 S 0.0718 0.0993 0.8289 59 L 0.0487 0.1080 0.8433 60 R 0.0289 0.0831 0.8880 61 T 0.0235 0.0665 0.9099 62 P 0.0076 0.6427 0.3497 63 Q 0.0068 0.7308 0.2624 64 S 0.0082 0.7872 0.2045 65 R 0.0074 0.8045 0.1882 66 T 0.0054 0.8250 0.1695 67 R 0.0038 0.9585 0.0377 68 A 0.0038 0.9612 0.0350 69 V 0.0038 0.9708 0.0255 70 A 0.0038 0.9732 0.0231 71 D 0.0038 0.9724 0.0239 72 V 0.0037 0.9723 0.0240 73 V 0.0038 0.9707 0.0256 74 D 0.0038 0.9657 0.0306 75 R 0.0038 0.9616 0.0347 76 L 0.0038 0.9592 0.0371 77 A 0.0038 0.9376 0.0586 78 D 0.0041 0.8432 0.1527 79 E 0.0053 0.4080 0.5867 80 G 0.0091 0.0428 0.9481 81 V 0.0335 0.0438 0.9227 82 V 0.0786 0.0559 0.8655 83 P 0.0588 0.1480 0.7932 84 A 0.0784 0.1918 0.7298 85 P 0.1338 0.2278 0.6384 86 R 0.1860 0.2360 0.5780 87 G 0.1842 0.2177 0.5982 88 E 0.2466 0.1581 0.5953 89 L 0.2992 0.1108 0.5900 90 Y 0.3697 0.0733 0.5569 91 R 0.4747 0.0558 0.4695 92 V 0.5838 0.0409 0.3753 93 N 0.6225 0.0259 0.3516 94 Q 0.3882 0.0301 0.5817 95 S 0.0817 0.0627 0.8557 96 W 0.0246 0.0609 0.9144 97 G 0.0256 0.0473 0.9271 98 E 0.0657 0.0274 0.9069 99 P 0.2328 0.0192 0.7481 100 T 0.5720 0.0196 0.4084 101 L 0.7729 0.0225 0.2046 102 M 0.8802 0.0287 0.0911 103 L 0.8983 0.0378 0.0640 104 L 0.8581 0.0539 0.0880 105 D 0.7087 0.1215 0.1697 106 R 0.3885 0.2854 0.3261 107 A 0.1749 0.4284 0.3968 108 V 0.1331 0.4983 0.3686 109 V 0.0770 0.5182 0.4048 110 P 0.0480 0.4943 0.4577 111 T 0.0290 0.5142 0.4569 112 F 0.0446 0.3680 0.5874 113 G 0.1237 0.1446 0.7318 114 V 0.3342 0.1125 0.5533 115 R 0.5256 0.1074 0.3669 116 A 0.5573 0.0872 0.3554 117 Y 0.5508 0.0935 0.3557 118 G 0.7007 0.0429 0.2563 119 V 0.8808 0.0149 0.1042 120 H 0.9323 0.0097 0.0579 121 L 0.9491 0.0062 0.0447 122 N 0.9536 0.0053 0.0411 123 G 0.9485 0.0039 0.0475 124 Y 0.9532 0.0031 0.0437 125 V 0.9319 0.0031 0.0650 126 G 0.7625 0.0052 0.2323 127 A 0.2908 0.0244 0.6848 128 G 0.0241 0.0501 0.9258 129 A 0.0233 0.0499 0.9268 130 D 0.2111 0.0300 0.7589 131 L 0.6507 0.0066 0.3426 132 H 0.8886 0.0026 0.1088 133 L 0.9554 0.0024 0.0422 134 W 0.9515 0.0028 0.0456 135 I 0.9080 0.0051 0.0870 136 G 0.7778 0.0068 0.2154 137 R 0.5677 0.0152 0.4171 138 R 0.4406 0.0233 0.5361 139 S 0.1386 0.0357 0.8257 140 P 0.0589 0.0692 0.8718 141 D 0.0283 0.0658 0.9060 142 K 0.0475 0.0694 0.8830 143 S 0.0725 0.0714 0.8561 144 V 0.1562 0.0733 0.7705 145 A 0.0585 0.0319 0.9096 146 P 0.0134 0.1704 0.8162 147 G 0.0139 0.1524 0.8337 148 K 0.0676 0.2695 0.6629 149 L 0.1327 0.3145 0.5528 150 D 0.1402 0.3501 0.5097 151 N 0.2132 0.4257 0.3611 152 M 0.2711 0.4317 0.2972 153 V 0.2691 0.3906 0.3403 154 A 0.1854 0.2949 0.5197 155 G 0.0895 0.1276 0.7829 156 G 0.0837 0.0679 0.8485 157 Q 0.1418 0.0754 0.7827 158 P 0.0829 0.1092 0.8079 159 A 0.0240 0.1261 0.8499 160 D 0.0155 0.0898 0.8947 161 L 0.0270 0.0787 0.8943 162 S 0.0336 0.0686 0.8978 163 L 0.0043 0.8782 0.1175 164 R 0.0038 0.9414 0.0548 165 Q 0.0038 0.9611 0.0352 166 N 0.0037 0.9696 0.0267 167 L 0.0037 0.9701 0.0261 168 I 0.0037 0.9697 0.0266 169 K 0.0038 0.9660 0.0302 170 E 0.0038 0.9593 0.0369 171 C 0.0038 0.9602 0.0360 172 A 0.0038 0.9421 0.0541 173 E 0.0040 0.8951 0.1009 174 E 0.0050 0.8307 0.1643 175 A 0.0064 0.5706 0.4230 176 D 0.0145 0.1132 0.8723 177 L 0.0244 0.0291 0.9465 178 P 0.0137 0.0336 0.9527 179 E 0.0043 0.8865 0.1092 180 A 0.0049 0.9068 0.0883 181 L 0.0045 0.9269 0.0686 182 A 0.0055 0.9165 0.0781 183 R 0.0050 0.7972 0.1977 184 Q 0.0059 0.6122 0.3819 185 A 0.0257 0.3322 0.6421 186 I 0.0544 0.1538 0.7918 187 P 0.1157 0.1084 0.7759 188 V 0.2687 0.0742 0.6571 189 G 0.5038 0.0388 0.4574 190 A 0.8295 0.0143 0.1562 191 I 0.9193 0.0101 0.0706 192 T 0.9141 0.0126 0.0733 193 Y 0.8703 0.0180 0.1118 194 C 0.8047 0.0214 0.1738 195 M 0.7051 0.0230 0.2719 196 E 0.5110 0.0278 0.4612 197 S 0.1783 0.0537 0.7680 198 P 0.0441 0.1373 0.8186 199 A 0.0217 0.1376 0.8408 200 G 0.0753 0.0920 0.8327 201 I 0.2456 0.0352 0.7191 202 K 0.2632 0.0162 0.7206 203 P 0.2618 0.0840 0.6542 204 D 0.4809 0.0689 0.4502 205 T 0.8277 0.0202 0.1521 206 L 0.9343 0.0086 0.0570 207 F 0.9612 0.0085 0.0303 208 L 0.9359 0.0140 0.0502 209 Y 0.8463 0.0132 0.1405 210 D 0.7341 0.0155 0.2504 211 L 0.6117 0.0146 0.3737 212 A 0.5733 0.0121 0.4146 213 L 0.3084 0.0108 0.6808 214 P 0.0813 0.0175 0.9012 215 E 0.0290 0.0963 0.8747 216 D 0.0249 0.0921 0.8830 217 F 0.1701 0.0547 0.7752 218 R 0.3085 0.0137 0.6779 219 P 0.2582 0.0137 0.7281 220 H 0.2150 0.0150 0.7700 221 N 0.0837 0.0211 0.8952 222 T 0.0598 0.0300 0.9101 223 D 0.0630 0.0618 0.8752 224 G 0.1324 0.1035 0.7642 225 E 0.3573 0.1510 0.4917 226 M 0.4702 0.1833 0.3465 227 A 0.5849 0.1540 0.2611 228 D 0.5517 0.1957 0.2526 229 F 0.6286 0.0892 0.2822 230 M 0.7428 0.0585 0.1987 231 L 0.7273 0.0326 0.2401 232 W 0.4896 0.0155 0.4949 233 P 0.2014 0.0220 0.7766 234 A 0.0044 0.9459 0.0497 235 A 0.0038 0.9625 0.0337 236 K 0.0037 0.9713 0.0250 237 V 0.0038 0.9708 0.0255 238 V 0.0037 0.9700 0.0262 239 E 0.0038 0.9623 0.0340 240 A 0.0038 0.9558 0.0405 241 V 0.0074 0.9255 0.0671 242 R 0.0062 0.8499 0.1439 243 T 0.0066 0.6895 0.3039 244 T 0.0094 0.3466 0.6440 245 E 0.0171 0.0735 0.9094 246 A 0.0652 0.0358 0.8991 247 F 0.2232 0.0340 0.7428 248 K 0.1177 0.0331 0.8492 249 F 0.0506 0.2738 0.6756 250 N 0.0312 0.3231 0.6456 251 V 0.0636 0.5265 0.4099 252 N 0.1070 0.6953 0.1977 253 L 0.2022 0.7286 0.0692 254 T 0.1889 0.7758 0.0353 255 V 0.1303 0.8387 0.0310 256 I 0.0343 0.9410 0.0247 257 D 0.0232 0.9495 0.0273 258 F 0.0234 0.9395 0.0371 259 A 0.0237 0.9201 0.0562 260 I 0.0276 0.9044 0.0680 261 R 0.0192 0.8510 0.1299 262 H 0.0353 0.4581 0.5066 263 G 0.0403 0.0882 0.8715 264 L 0.1164 0.0735 0.8102 265 I 0.2471 0.0524 0.7005 266 D 0.0754 0.0421 0.8826 267 P 0.0085 0.3288 0.6627 268 D 0.0060 0.2878 0.7062 269 N 0.0102 0.2868 0.7030 270 E 0.0152 0.2263 0.7585 271 P 0.0139 0.3915 0.5946 272 D 0.0342 0.4285 0.5373 273 Y 0.0081 0.9057 0.0862 274 Q 0.0058 0.9567 0.0375 275 E 0.0044 0.9647 0.0309 276 I 0.0040 0.9642 0.0318 277 L 0.0037 0.9548 0.0415 278 A 0.0044 0.9274 0.0682 279 G 0.0043 0.8307 0.1650 280 L 0.0202 0.6424 0.3373 281 R 0.0412 0.4154 0.5433 282 G 0.0645 0.2477 0.6878 283 R 0.0792 0.1611 0.7596 284 P 0.0714 0.0397 0.8889 285 R 0.0637 0.0190 0.9172 286 E 0.0713 0.0207 0.9080 287 R 0.0806 0.0265 0.8929 288 A 0.0755 0.0346 0.8899 289 A 0.0518 0.0357 0.9125 290 S 0.0316 0.0323 0.9362 291 P 0.0244 0.0239 0.9517 292 A 0.0098 0.0055 0.9847