# This file is the result of combining several RDB files, specifically # T0293.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0293.t2k.stride-ebghtl.rdb (weight 1.24869) # T0293.t2k.str2.rdb (weight 1.54758) # T0293.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 T0293.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 396 # # ============================================ # Comments from T0293.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 396 # # ============================================ # Comments from T0293.t2k.str2.rdb # ============================================ # TARGET T0293 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0293.t2k-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 396 # # ============================================ # Comments from T0293.t2k.alpha.rdb # ============================================ # TARGET T0293 # 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 T0293.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 396 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.3241 0.0181 0.6578 2 S 0.4551 0.0421 0.5028 3 L 0.4752 0.1275 0.3974 4 N 0.4061 0.1355 0.4584 5 F 0.2056 0.2244 0.5700 6 K 0.1022 0.2211 0.6767 7 D 0.0599 0.1671 0.7731 8 P 0.0139 0.5957 0.3905 9 E 0.0181 0.5717 0.4102 10 A 0.0279 0.5930 0.3791 11 V 0.0763 0.5409 0.3827 12 R 0.0547 0.7122 0.2331 13 A 0.0292 0.8816 0.0892 14 L 0.0221 0.8987 0.0792 15 T 0.0184 0.9114 0.0703 16 C 0.0157 0.9151 0.0692 17 T 0.0328 0.8590 0.1082 18 L 0.0251 0.8195 0.1553 19 L 0.0294 0.8016 0.1690 20 R 0.0376 0.7537 0.2086 21 E 0.0302 0.7066 0.2631 22 D 0.0472 0.5242 0.4285 23 F 0.0734 0.3371 0.5895 24 G 0.0893 0.0700 0.8407 25 L 0.2021 0.0332 0.7648 26 S 0.4660 0.0313 0.5028 27 I 0.6856 0.0193 0.2951 28 D 0.7290 0.0147 0.2563 29 I 0.5582 0.0127 0.4291 30 P 0.2018 0.0183 0.7798 31 L 0.0280 0.1935 0.7785 32 E 0.0243 0.1501 0.8256 33 R 0.1703 0.1865 0.6432 34 L 0.3887 0.0429 0.5684 35 I 0.3507 0.0275 0.6218 36 P 0.2810 0.0275 0.6915 37 T 0.1201 0.0382 0.8416 38 V 0.0690 0.0974 0.8335 39 P 0.0396 0.3946 0.5657 40 L 0.0357 0.5331 0.4312 41 R 0.0213 0.7920 0.1867 42 L 0.0145 0.8634 0.1221 43 N 0.0130 0.8844 0.1025 44 Y 0.0090 0.9344 0.0566 45 I 0.0084 0.9454 0.0462 46 H 0.0085 0.9415 0.0499 47 W 0.0089 0.9451 0.0461 48 V 0.0075 0.9452 0.0473 49 E 0.0057 0.9451 0.0492 50 D 0.0055 0.9401 0.0545 51 L 0.0067 0.9194 0.0739 52 I 0.0104 0.8445 0.1451 53 G 0.0131 0.6808 0.3062 54 H 0.0246 0.5150 0.4603 55 Q 0.0472 0.3098 0.6431 56 D 0.0621 0.2744 0.6634 57 S 0.0662 0.2784 0.6554 58 D 0.0667 0.2563 0.6770 59 K 0.0613 0.3011 0.6375 60 S 0.0555 0.2282 0.7164 61 T 0.0830 0.1828 0.7342 62 L 0.1686 0.1045 0.7268 63 R 0.3278 0.0425 0.6298 64 R 0.7453 0.0210 0.2337 65 G 0.8477 0.0280 0.1243 66 I 0.8460 0.0277 0.1263 67 D 0.7956 0.0261 0.1783 68 I 0.4648 0.0788 0.4564 69 G 0.1951 0.0938 0.7111 70 T 0.0861 0.1980 0.7159 71 G 0.0551 0.3009 0.6440 72 A 0.0239 0.6568 0.3194 73 S 0.0156 0.7418 0.2426 74 C 0.0069 0.9396 0.0535 75 I 0.0048 0.9541 0.0411 76 Y 0.0054 0.9558 0.0389 77 P 0.0063 0.9522 0.0415 78 L 0.0064 0.9459 0.0477 79 L 0.0103 0.9263 0.0633 80 G 0.0111 0.8894 0.0995 81 A 0.0246 0.7808 0.1946 82 T 0.0383 0.6060 0.3557 83 L 0.0746 0.1918 0.7337 84 N 0.0252 0.1312 0.8436 85 G 0.0328 0.0687 0.8986 86 W 0.2616 0.0181 0.7203 87 Y 0.7915 0.0070 0.2015 88 F 0.9197 0.0032 0.0771 89 L 0.9025 0.0114 0.0860 90 A 0.9010 0.0066 0.0924 91 T 0.8141 0.0106 0.1753 92 E 0.5489 0.0185 0.4326 93 V 0.0962 0.0814 0.8223 94 D 0.0671 0.1056 0.8274 95 D 0.0051 0.9245 0.0704 96 M 0.0049 0.9475 0.0476 97 C 0.0048 0.9553 0.0399 98 F 0.0047 0.9603 0.0350 99 N 0.0047 0.9604 0.0349 100 Y 0.0047 0.9602 0.0351 101 A 0.0047 0.9599 0.0354 102 K 0.0047 0.9599 0.0354 103 K 0.0047 0.9571 0.0382 104 N 0.0047 0.9491 0.0462 105 V 0.0049 0.9447 0.0505 106 E 0.0052 0.9327 0.0620 107 Q 0.0108 0.8257 0.1635 108 N 0.0487 0.4054 0.5459 109 N 0.0595 0.1154 0.8251 110 L 0.0452 0.2519 0.7029 111 S 0.0361 0.3838 0.5801 112 D 0.0665 0.3883 0.5453 113 L 0.3530 0.1948 0.4522 114 I 0.6906 0.0631 0.2463 115 K 0.8064 0.0652 0.1284 116 V 0.8216 0.0652 0.1131 117 V 0.7057 0.1057 0.1886 118 K 0.5023 0.1298 0.3678 119 V 0.1707 0.1567 0.6726 120 P 0.1185 0.1833 0.6982 121 Q 0.0512 0.4936 0.4552 122 A 0.0438 0.5028 0.4534 123 T 0.0499 0.5287 0.4215 124 L 0.0776 0.5154 0.4070 125 L 0.1125 0.4660 0.4215 126 M 0.1030 0.5424 0.3547 127 D 0.0839 0.5461 0.3700 128 A 0.0610 0.5128 0.4261 129 L 0.0795 0.3840 0.5365 130 K 0.1406 0.3188 0.5406 131 E 0.1321 0.3026 0.5654 132 E 0.1064 0.2427 0.6510 133 S 0.0701 0.2418 0.6881 134 E 0.0706 0.1442 0.7852 135 I 0.2107 0.0847 0.7046 136 I 0.4823 0.0423 0.4755 137 Y 0.5861 0.0083 0.4055 138 D 0.7237 0.0275 0.2489 139 F 0.9183 0.0046 0.0771 140 C 0.9249 0.0044 0.0707 141 M 0.9080 0.0074 0.0847 142 C 0.7380 0.0103 0.2516 143 N 0.2476 0.0198 0.7326 144 P 0.1021 0.0825 0.8154 145 P 0.0737 0.2488 0.6775 146 F 0.0761 0.3162 0.6076 147 F 0.0983 0.2536 0.6481 148 A 0.0583 0.3205 0.6212 149 N 0.0405 0.4913 0.4682 150 Q 0.0238 0.6529 0.3234 151 L 0.0233 0.7168 0.2599 152 E 0.0219 0.7450 0.2331 153 A 0.0248 0.7185 0.2567 154 K 0.0330 0.5828 0.3842 155 G 0.0525 0.4171 0.5304 156 V 0.0645 0.3783 0.5572 157 N 0.0474 0.4976 0.4550 158 S 0.0803 0.4988 0.4209 159 R 0.1312 0.4390 0.4297 160 N 0.0953 0.3726 0.5321 161 P 0.0654 0.4148 0.5198 162 R 0.0490 0.3796 0.5713 163 R 0.0608 0.2793 0.6598 164 P 0.0562 0.2298 0.7139 165 P 0.0487 0.2718 0.6795 166 P 0.0429 0.4487 0.5085 167 S 0.0486 0.4593 0.4921 168 S 0.0632 0.4572 0.4796 169 V 0.0599 0.3850 0.5551 170 N 0.0489 0.2806 0.6705 171 T 0.0562 0.2352 0.7086 172 G 0.0652 0.1895 0.7453 173 G 0.0989 0.3048 0.5963 174 I 0.0836 0.6734 0.2430 175 T 0.1005 0.7251 0.1744 176 E 0.1482 0.7162 0.1356 177 I 0.1817 0.6532 0.1652 178 M 0.1731 0.5538 0.2731 179 A 0.1118 0.4012 0.4870 180 E 0.0430 0.2335 0.7235 181 G 0.0269 0.2447 0.7284 182 G 0.0359 0.2739 0.6902 183 E 0.0387 0.6274 0.3339 184 L 0.0200 0.8661 0.1139 185 E 0.0139 0.9172 0.0690 186 F 0.0101 0.9325 0.0574 187 V 0.0072 0.9485 0.0443 188 K 0.0067 0.9524 0.0410 189 R 0.0053 0.9472 0.0475 190 I 0.0048 0.9511 0.0441 191 I 0.0048 0.9514 0.0438 192 H 0.0049 0.9492 0.0459 193 D 0.0055 0.9349 0.0596 194 S 0.0061 0.9311 0.0627 195 L 0.0054 0.9234 0.0713 196 Q 0.0066 0.8690 0.1244 197 L 0.0125 0.7374 0.2500 198 G 0.0626 0.4638 0.4736 199 K 0.0730 0.2401 0.6870 200 R 0.0505 0.1953 0.7542 201 L 0.1157 0.0573 0.8270 202 R 0.4218 0.0177 0.5604 203 W 0.8185 0.0051 0.1764 204 Y 0.9026 0.0034 0.0940 205 S 0.9168 0.0035 0.0797 206 C 0.8985 0.0040 0.0975 207 M 0.8524 0.0058 0.1418 208 L 0.5636 0.0172 0.4192 209 G 0.1880 0.0392 0.7728 210 K 0.0344 0.3554 0.6102 211 A 0.0318 0.4667 0.5016 212 C 0.0364 0.4489 0.5148 213 S 0.0445 0.4053 0.5503 214 L 0.0264 0.6263 0.3472 215 A 0.0189 0.7066 0.2745 216 P 0.0139 0.8567 0.1294 217 L 0.0106 0.9108 0.0786 218 K 0.0070 0.9363 0.0567 219 E 0.0061 0.9488 0.0451 220 E 0.0056 0.9442 0.0502 221 L 0.0056 0.9357 0.0587 222 R 0.0080 0.8793 0.1127 223 I 0.0323 0.6234 0.3443 224 Q 0.0498 0.1810 0.7691 225 G 0.0599 0.0540 0.8860 226 V 0.1474 0.0323 0.8203 227 P 0.2492 0.0396 0.7113 228 K 0.6462 0.0278 0.3260 229 V 0.8542 0.0091 0.1367 230 T 0.8683 0.0087 0.1230 231 Y 0.8615 0.0086 0.1300 232 T 0.8256 0.0136 0.1607 233 E 0.7656 0.0230 0.2114 234 F 0.4718 0.0547 0.4736 235 C 0.2007 0.1054 0.6939 236 Q 0.0846 0.0628 0.8527 237 G 0.0671 0.0479 0.8849 238 R 0.2594 0.0342 0.7064 239 T 0.6596 0.0354 0.3050 240 M 0.7811 0.0342 0.1847 241 R 0.8063 0.0397 0.1539 242 W 0.8829 0.0264 0.0907 243 A 0.9095 0.0152 0.0753 244 L 0.9046 0.0215 0.0739 245 A 0.8842 0.0301 0.0858 246 W 0.8021 0.0618 0.1362 247 S 0.6882 0.0739 0.2379 248 F 0.4862 0.0678 0.4460 249 Y 0.2147 0.0469 0.7384 250 D 0.0781 0.0229 0.8990