# This file is the result of combining several RDB files, specifically # T0470.t2k.str2.rdb (weight 1.54425) # T0470.t2k.str4.rdb (weight 0.924988) # T0470.t2k.pb.rdb (weight 0.789901) # T0470.t2k.bys.rdb (weight 0.748322) # T0470.t2k.alpha.rdb (weight 0.678173) # 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 T0470.t2k.str2.rdb # ============================================ # TARGET T0470 # Using neural net dunbrack-40pc-3157-t2k-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 T0470.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 78.502 # # ============================================ # Comments from T0470.t2k.str4.rdb # ============================================ # TARGET T0470 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0470.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 78.502 # # ============================================ # Comments from T0470.t2k.pb.rdb # ============================================ # TARGET T0470 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0470.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 78.502 # # ============================================ # Comments from T0470.t2k.bys.rdb # ============================================ # TARGET T0470 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0470.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 78.502 # # ============================================ # Comments from T0470.t2k.alpha.rdb # ============================================ # TARGET T0470 # Using neural net dunbrack-40pc-3157-t2k-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 T0470.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 78.502 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1901 0.1593 0.6506 2 T 0.1542 0.1885 0.6573 3 K 0.0509 0.6231 0.3260 4 Q 0.0233 0.8027 0.1741 5 E 0.0117 0.8970 0.0913 6 K 0.0092 0.9121 0.0787 7 I 0.0084 0.9206 0.0710 8 E 0.0083 0.9230 0.0688 9 K 0.0083 0.9232 0.0685 10 T 0.0083 0.9220 0.0696 11 I 0.0083 0.9221 0.0696 12 T 0.0083 0.9234 0.0684 13 F 0.0083 0.9222 0.0695 14 V 0.0084 0.9171 0.0745 15 K 0.0085 0.9139 0.0776 16 H 0.0094 0.9038 0.0868 17 I 0.0190 0.8489 0.1320 18 L 0.0304 0.7770 0.1926 19 E 0.0335 0.6427 0.3238 20 K 0.0525 0.4369 0.5106 21 D 0.0858 0.3273 0.5869 22 A 0.0746 0.3272 0.5982 23 S 0.0781 0.2970 0.6249 24 G 0.0894 0.2473 0.6633 25 H 0.1391 0.2370 0.6239 26 D 0.1340 0.2620 0.6040 27 W 0.0317 0.7156 0.2527 28 Y 0.0221 0.7958 0.1821 29 H 0.0167 0.8681 0.1152 30 I 0.0106 0.8989 0.0905 31 R 0.0084 0.9152 0.0764 32 R 0.0083 0.9234 0.0683 33 V 0.0083 0.9226 0.0692 34 H 0.0083 0.9222 0.0695 35 K 0.0083 0.9239 0.0678 36 M 0.0083 0.9236 0.0681 37 A 0.0084 0.9170 0.0746 38 I 0.0083 0.9192 0.0724 39 S 0.0086 0.9125 0.0789 40 L 0.0102 0.8947 0.0951 41 S 0.0104 0.8668 0.1228 42 E 0.0131 0.7997 0.1872 43 Q 0.0293 0.6629 0.3078 44 E 0.0725 0.3106 0.6169 45 G 0.0484 0.1270 0.8247 46 G 0.1169 0.1553 0.7277 47 N 0.0995 0.3389 0.5617 48 R 0.0405 0.7271 0.2324 49 F 0.0322 0.8317 0.1360 50 I 0.0231 0.8919 0.0850 51 I 0.0144 0.9113 0.0743 52 E 0.0101 0.9208 0.0691 53 M 0.0093 0.9189 0.0718 54 A 0.0090 0.9145 0.0765 55 A 0.0105 0.8985 0.0910 56 L 0.0146 0.8600 0.1254 57 L 0.0275 0.7470 0.2255 58 H 0.0540 0.6254 0.3206 59 D 0.0686 0.5288 0.4025 60 V 0.0606 0.5855 0.3539 61 A 0.0986 0.4784 0.4230 62 D 0.1195 0.3838 0.4967 63 E 0.0707 0.5997 0.3296 64 K 0.0880 0.5508 0.3612 65 L 0.1158 0.4114 0.4728 66 N 0.1274 0.2414 0.6312 67 E 0.1305 0.2761 0.5935 68 S 0.1070 0.3626 0.5303 69 E 0.0448 0.6036 0.3516 70 E 0.0438 0.6904 0.2658 71 A 0.0416 0.7278 0.2306 72 G 0.0267 0.7839 0.1894 73 M 0.0132 0.8675 0.1193 74 K 0.0097 0.8995 0.0908 75 K 0.0089 0.9108 0.0802 76 V 0.0090 0.9103 0.0808 77 S 0.0084 0.9178 0.0738 78 D 0.0084 0.9186 0.0729 79 W 0.0094 0.9090 0.0815 80 L 0.0098 0.8924 0.0977 81 E 0.0098 0.8529 0.1374 82 E 0.0167 0.7108 0.2725 83 L 0.0566 0.3626 0.5808 84 H 0.0631 0.1388 0.7981 85 V 0.1582 0.0656 0.7762 86 E 0.1507 0.1164 0.7329 87 E 0.0149 0.7369 0.2482 88 E 0.0112 0.8515 0.1373 89 E 0.0131 0.8911 0.0958 90 S 0.0093 0.9088 0.0819 91 K 0.0088 0.9165 0.0747 92 H 0.0087 0.9209 0.0704 93 V 0.0084 0.9171 0.0745 94 L 0.0083 0.9212 0.0704 95 H 0.0083 0.9235 0.0683 96 I 0.0085 0.9170 0.0744 97 I 0.0099 0.8979 0.0923 98 A 0.0147 0.8392 0.1461 99 N 0.0383 0.6495 0.3122 100 M 0.1376 0.4156 0.4468 101 S 0.2028 0.2688 0.5284 102 Y 0.1995 0.2376 0.5629 103 K 0.1885 0.2170 0.5945 104 G 0.1374 0.2030 0.6596 105 G 0.1342 0.1562 0.7097 106 H 0.1527 0.1515 0.6958 107 G 0.1160 0.1374 0.7466 108 G 0.1429 0.1199 0.7372 109 K 0.2487 0.0532 0.6980 110 V 0.3158 0.0914 0.5928 111 E 0.3334 0.0989 0.5677 112 S 0.3259 0.0929 0.5812 113 I 0.2226 0.3150 0.4623 114 E 0.3090 0.3259 0.3651 115 G 0.4038 0.2440 0.3522 116 K 0.4864 0.2262 0.2874 117 L 0.3765 0.2902 0.3333 118 V 0.2517 0.3846 0.3637 119 Q 0.1898 0.4266 0.3836 120 D 0.1057 0.4287 0.4656 121 A 0.0382 0.6571 0.3048 122 D 0.0214 0.7310 0.2476 123 R 0.0194 0.8098 0.1708 124 L 0.0140 0.8738 0.1123 125 D 0.0116 0.8762 0.1122 126 A 0.0221 0.8205 0.1574 127 L 0.0302 0.7096 0.2603 128 G 0.0384 0.6294 0.3323 129 A 0.0490 0.7532 0.1978 130 I 0.0541 0.7714 0.1745 131 G 0.0468 0.8013 0.1519 132 I 0.0406 0.8388 0.1206 133 A 0.0458 0.8406 0.1136 134 R 0.0428 0.8489 0.1082 135 T 0.0701 0.8114 0.1184 136 F 0.1091 0.7438 0.1472 137 A 0.1364 0.6699 0.1937 138 Y 0.1677 0.5595 0.2728 139 G 0.1335 0.4488 0.4177 140 G 0.1163 0.3371 0.5466 141 A 0.1102 0.4197 0.4702 142 K 0.0982 0.2071 0.6948 143 G 0.0856 0.1275 0.7869 144 R 0.2424 0.0988 0.6588 145 L 0.3770 0.1514 0.4715 146 M 0.4190 0.1530 0.4279 147 Y 0.3883 0.0997 0.5120 148 D 0.2228 0.0473 0.7299 149 P 0.0485 0.3712 0.5803 150 T 0.0810 0.2402 0.6788 151 I 0.1977 0.0634 0.7388 152 P 0.1666 0.0684 0.7650 153 P 0.1262 0.3475 0.5263 154 R 0.0794 0.5911 0.3295 155 E 0.1050 0.5949 0.3001 156 V 0.1466 0.4723 0.3811 157 M 0.1999 0.3404 0.4596 158 T 0.1757 0.2718 0.5525 159 K 0.0324 0.6663 0.3013 160 D 0.0343 0.7233 0.2423 161 E 0.0624 0.7131 0.2245 162 Y 0.0782 0.6653 0.2565 163 R 0.0899 0.5425 0.3677 164 K 0.0727 0.3924 0.5348 165 N 0.0807 0.2524 0.6669 166 N 0.0898 0.2228 0.6874 167 D 0.1435 0.2156 0.6409 168 P 0.0574 0.5437 0.3988 169 S 0.0629 0.6647 0.2723 170 L 0.0345 0.8240 0.1415 171 N 0.0166 0.8747 0.1087 172 H 0.0128 0.9040 0.0832 173 F 0.0100 0.9128 0.0772 174 Y 0.0085 0.9201 0.0714 175 E 0.0084 0.9188 0.0728 176 K 0.0087 0.9131 0.0782 177 L 0.0118 0.8679 0.1203 178 L 0.0177 0.8067 0.1756 179 K 0.0360 0.6540 0.3100 180 L 0.0420 0.6419 0.3161 181 K 0.0197 0.7807 0.1996 182 D 0.0191 0.7353 0.2457 183 L 0.0374 0.6606 0.3021 184 M 0.1115 0.5245 0.3639 185 N 0.1236 0.3710 0.5054 186 T 0.1074 0.3640 0.5287 187 N 0.0181 0.7172 0.2648 188 A 0.0129 0.8233 0.1638 189 A 0.0113 0.8980 0.0907 190 K 0.0086 0.9128 0.0786 191 Q 0.0084 0.9166 0.0751 192 E 0.0087 0.9150 0.0764 193 A 0.0088 0.9172 0.0740 194 E 0.0084 0.9201 0.0715 195 V 0.0085 0.9185 0.0729 196 R 0.0086 0.9173 0.0741 197 H 0.0084 0.9197 0.0719 198 R 0.0083 0.9224 0.0693 199 Y 0.0083 0.9231 0.0686 200 M 0.0083 0.9207 0.0710 201 E 0.0083 0.9237 0.0680 202 Q 0.0083 0.9247 0.0671 203 F 0.0083 0.9230 0.0687 204 I 0.0083 0.9197 0.0719 205 E 0.0083 0.9236 0.0682 206 Q 0.0083 0.9220 0.0697 207 F 0.0084 0.9158 0.0758 208 M 0.0085 0.9108 0.0808 209 K 0.0087 0.8959 0.0953 210 E 0.0120 0.8258 0.1621 211 W 0.0379 0.7037 0.2584 212 N 0.0415 0.5043 0.4542 213 A 0.0510 0.5696 0.3794 214 Q 0.0970 0.5056 0.3974 215 I 0.1574 0.4874 0.3552 216 L 0.1963 0.4269 0.3768 217 E 0.2304 0.3477 0.4219 218 H 0.2235 0.2985 0.4780 219 H 0.1929 0.2459 0.5612 220 H 0.1723 0.2537 0.5740 221 H 0.1729 0.2130 0.6141 222 H 0.1874 0.1717 0.6408 223 H 0.1858 0.1332 0.6810