# This file is the result of combining several RDB files, specifically # T0320.t06.dssp-ebghstl.rdb (weight 1.53986) # T0320.t06.stride-ebghtl.rdb (weight 1.24869) # T0320.t06.str2.rdb (weight 1.54758) # T0320.t06.alpha.rdb (weight 0.659012) # T0320.t04.dssp-ebghstl.rdb (weight 1.53986) # T0320.t04.stride-ebghtl.rdb (weight 1.24869) # T0320.t04.str2.rdb (weight 1.54758) # T0320.t04.alpha.rdb (weight 0.659012) # T0320.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0320.t2k.stride-ebghtl.rdb (weight 1.24869) # T0320.t2k.str2.rdb (weight 1.54758) # T0320.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 T0320.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0320 # Using neural net t04-2621-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 T0320.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 2603 # # ============================================ # Comments from T0320.t06.stride-ebghtl.rdb # ============================================ # TARGET T0320 # Using neural net t04-2621-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 T0320.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 2603 # # ============================================ # Comments from T0320.t06.str2.rdb # ============================================ # TARGET T0320 # 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 T0320.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 2603 # # ============================================ # Comments from T0320.t06.alpha.rdb # ============================================ # TARGET T0320 # Using neural net t04-2621-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 T0320.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 2603 # # ============================================ # Comments from T0320.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0320 # Using neural net t04-2621-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 T0320.t04-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 1874 # # ============================================ # Comments from T0320.t04.stride-ebghtl.rdb # ============================================ # TARGET T0320 # Using neural net t04-2621-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 T0320.t04-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 1874 # # ============================================ # Comments from T0320.t04.str2.rdb # ============================================ # TARGET T0320 # 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 T0320.t04-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 1874 # # ============================================ # Comments from T0320.t04.alpha.rdb # ============================================ # TARGET T0320 # Using neural net t04-2621-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 T0320.t04-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 1874 # # ============================================ # Comments from T0320.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0320 # 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 T0320.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 223 # # ============================================ # Comments from T0320.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0320 # 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 T0320.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 223 # # ============================================ # Comments from T0320.t2k.str2.rdb # ============================================ # TARGET T0320 # 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 T0320.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 223 # # ============================================ # Comments from T0320.t2k.alpha.rdb # ============================================ # TARGET T0320 # 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 T0320.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 223 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0741 0.1075 0.8184 2 Q 0.1311 0.0751 0.7938 3 L 0.0984 0.0317 0.8699 4 S 0.1118 0.1034 0.7848 5 K 0.1288 0.2263 0.6449 6 A 0.2190 0.2358 0.5452 7 A 0.3952 0.1511 0.4537 8 E 0.5098 0.1303 0.3599 9 M 0.3802 0.1439 0.4759 10 C 0.2613 0.2041 0.5347 11 Y 0.2610 0.2303 0.5087 12 E 0.3721 0.2009 0.4269 13 I 0.2990 0.2193 0.4816 14 T 0.2267 0.2278 0.5455 15 N 0.1613 0.3177 0.5211 16 S 0.1069 0.4999 0.3932 17 Y 0.1137 0.5118 0.3745 18 L 0.0834 0.5580 0.3586 19 H 0.0728 0.5574 0.3698 20 I 0.0549 0.6218 0.3233 21 D 0.0364 0.6773 0.2863 22 Q 0.0327 0.7020 0.2653 23 K 0.0309 0.7180 0.2511 24 S 0.0355 0.6951 0.2694 25 Q 0.0329 0.7400 0.2272 26 I 0.0154 0.8149 0.1697 27 I 0.0126 0.8237 0.1637 28 A 0.0109 0.8337 0.1554 29 S 0.0132 0.8079 0.1789 30 T 0.0109 0.8110 0.1781 31 Q 0.0087 0.8680 0.1233 32 E 0.0068 0.8915 0.1018 33 A 0.0062 0.8973 0.0965 34 I 0.0062 0.9080 0.0858 35 R 0.0063 0.8983 0.0955 36 L 0.0065 0.8850 0.1085 37 T 0.0071 0.8805 0.1124 38 R 0.0082 0.8183 0.1736 39 K 0.0101 0.7862 0.2037 40 Y 0.0140 0.7642 0.2218 41 L 0.0053 0.9059 0.0888 42 L 0.0049 0.9392 0.0559 43 S 0.0051 0.9492 0.0457 44 E 0.0050 0.9548 0.0402 45 I 0.0050 0.9526 0.0423 46 F 0.0057 0.9408 0.0535 47 V 0.0087 0.9071 0.0842 48 R 0.0311 0.8280 0.1409 49 W 0.0522 0.7301 0.2178 50 S 0.0827 0.6087 0.3086 51 P 0.0568 0.4570 0.4862 52 L 0.0632 0.1956 0.7412 53 N 0.0690 0.1083 0.8227 54 G 0.0569 0.1173 0.8258 55 E 0.2634 0.0623 0.6743 56 I 0.7243 0.0164 0.2593 57 S 0.8822 0.0101 0.1077 58 F 0.9112 0.0059 0.0829 59 S 0.8877 0.0097 0.1026 60 Y 0.7792 0.0216 0.1992 61 N 0.4687 0.0491 0.4822 62 G 0.1326 0.0708 0.7967 63 G 0.0615 0.1555 0.7831 64 K 0.0187 0.5222 0.4592 65 D 0.0180 0.6577 0.3243 66 C 0.0079 0.9266 0.0655 67 Q 0.0059 0.9531 0.0409 68 V 0.0071 0.9544 0.0385 69 L 0.0053 0.9587 0.0360 70 L 0.0068 0.9570 0.0362 71 L 0.0059 0.9579 0.0362 72 L 0.0050 0.9585 0.0365 73 Y 0.0048 0.9527 0.0425 74 L 0.0055 0.9224 0.0721 75 S 0.0088 0.8211 0.1701 76 C 0.0207 0.6051 0.3742 77 L 0.0642 0.2324 0.7034 78 W 0.0497 0.1585 0.7918 79 E 0.0532 0.1232 0.8237 80 Y 0.1162 0.0871 0.7967 81 F 0.2086 0.0204 0.7710 82 F 0.4411 0.0128 0.5461 83 I 0.8152 0.0086 0.1762 84 K 0.8870 0.0079 0.1052 85 A 0.8809 0.0073 0.1118 86 Q 0.7473 0.0207 0.2319 87 N 0.3547 0.0335 0.6119 88 S 0.1036 0.0880 0.8084 89 Q 0.0824 0.0897 0.8280 90 F 0.1100 0.1129 0.7771 91 D 0.1089 0.1044 0.7867 92 F 0.0929 0.1449 0.7622 93 E 0.0618 0.4202 0.5180 94 F 0.0930 0.5229 0.3841 95 Q 0.1134 0.5633 0.3233 96 S 0.0755 0.6250 0.2995 97 F 0.0451 0.5979 0.3571 98 P 0.0223 0.6576 0.3201 99 M 0.0134 0.7724 0.2143 100 Q 0.0091 0.8239 0.1670 101 R 0.0161 0.8100 0.1739 102 L 0.0275 0.7851 0.1874 103 P 0.0194 0.8259 0.1548 104 T 0.0433 0.7971 0.1596 105 V 0.0513 0.7002 0.2486 106 F 0.1258 0.4206 0.4536 107 I 0.1490 0.1872 0.6638 108 D 0.1371 0.1749 0.6881 109 Q 0.1803 0.1357 0.6840 110 E 0.2890 0.1539 0.5571 111 E 0.4405 0.1158 0.4437 112 T 0.3630 0.0968 0.5403 113 F 0.2654 0.0577 0.6769 114 P 0.1333 0.0712 0.7955 115 T 0.0836 0.1870 0.7294 116 L 0.0268 0.5464 0.4267 117 E 0.0223 0.6078 0.3699 118 N 0.0238 0.7431 0.2332 119 F 0.0288 0.8090 0.1623 120 V 0.0282 0.8472 0.1246 121 L 0.0271 0.8748 0.0981 122 E 0.0292 0.8683 0.1025 123 T 0.0241 0.8582 0.1177 124 S 0.0314 0.8007 0.1679 125 E 0.0260 0.7853 0.1887 126 R 0.0304 0.6879 0.2818 127 Y 0.0481 0.4693 0.4827 128 C 0.0774 0.2698 0.6528 129 L 0.0729 0.4280 0.4991 130 S 0.0810 0.4778 0.4412 131 L 0.1352 0.5206 0.3442 132 Y 0.2236 0.4204 0.3560 133 E 0.2600 0.3886 0.3515 134 S 0.2531 0.3691 0.3778 135 Q 0.1616 0.2964 0.5420 136 R 0.1145 0.1822 0.7033 137 Q 0.0893 0.1959 0.7148 138 S 0.1044 0.1460 0.7496 139 G 0.0465 0.3202 0.6333 140 A 0.0836 0.3505 0.5659 141 S 0.1567 0.3516 0.4917 142 V 0.2253 0.3024 0.4722 143 N 0.2617 0.2768 0.4615 144 M 0.2410 0.3020 0.4570 145 A 0.1718 0.4257 0.4024 146 D 0.1890 0.3866 0.4243 147 A 0.1738 0.3872 0.4390 148 F 0.0778 0.4974 0.4248 149 R 0.0571 0.5752 0.3677 150 D 0.0361 0.7783 0.1856 151 F 0.0207 0.8139 0.1655 152 I 0.0221 0.7949 0.1830 153 K 0.0222 0.7326 0.2452 154 I 0.0222 0.5572 0.4207 155 Y 0.0448 0.2237 0.7315 156 P 0.0212 0.1595 0.8193 157 E 0.0294 0.0859 0.8847 158 T 0.1697 0.0239 0.8063 159 E 0.5217 0.0216 0.4567 160 A 0.9113 0.0040 0.0846 161 I 0.9258 0.0034 0.0707 162 V 0.9243 0.0033 0.0724 163 I 0.8344 0.0201 0.1455 164 G 0.6599 0.0131 0.3270 165 I 0.4816 0.0249 0.4935 166 R 0.3676 0.0319 0.6005 167 H 0.2334 0.0844 0.6822 168 T 0.1044 0.0709 0.8246 169 D 0.0720 0.0479 0.8801 170 P 0.0505 0.2447 0.7048 171 F 0.0545 0.3633 0.5822 172 G 0.0788 0.4064 0.5148 173 E 0.0814 0.5145 0.4041 174 A 0.0938 0.4440 0.4622 175 L 0.1282 0.3299 0.5419 176 K 0.1497 0.0923 0.7580 177 P 0.1661 0.0622 0.7717 178 I 0.2761 0.0741 0.6499 179 Q 0.3416 0.0688 0.5896 180 R 0.3237 0.0720 0.6043 181 T 0.2052 0.0700 0.7247 182 D 0.0929 0.0568 0.8503 183 S 0.0278 0.1765 0.7957 184 N 0.0321 0.1298 0.8380 185 W 0.0666 0.1606 0.7729 186 P 0.0596 0.1469 0.7934 187 D 0.0783 0.2005 0.7213 188 F 0.3642 0.1478 0.4880 189 M 0.6448 0.0570 0.2982 190 R 0.7072 0.0508 0.2420 191 L 0.6012 0.0810 0.3178 192 Q 0.3660 0.1150 0.5190 193 P 0.1825 0.3484 0.4691 194 L 0.1772 0.3859 0.4369 195 L 0.1371 0.3850 0.4779 196 H 0.1577 0.2314 0.6109 197 W 0.1825 0.1330 0.6845 198 D 0.1755 0.0666 0.7579 199 L 0.0120 0.8790 0.1090 200 T 0.0054 0.9236 0.0710 201 N 0.0056 0.9419 0.0525 202 I 0.0047 0.9576 0.0377 203 W 0.0047 0.9588 0.0365 204 S 0.0047 0.9601 0.0352 205 F 0.0047 0.9595 0.0357 206 L 0.0050 0.9566 0.0384 207 L 0.0053 0.9377 0.0570 208 Y 0.0093 0.8507 0.1400 209 S 0.0423 0.4136 0.5441 210 N 0.0339 0.0302 0.9360 211 E 0.0791 0.0107 0.9102 212 P 0.1487 0.0193 0.8321 213 I 0.1926 0.1082 0.6991 214 C 0.1362 0.2411 0.6227 215 G 0.0715 0.5143 0.4142 216 L 0.0795 0.6024 0.3181 217 Y 0.0813 0.5669 0.3518 218 G 0.0809 0.4455 0.4737 219 K 0.0706 0.2126 0.7168 220 G 0.0674 0.0576 0.8750 221 F 0.2633 0.0363 0.7004 222 T 0.4136 0.0337 0.5527 223 S 0.4397 0.0467 0.5135 224 I 0.2882 0.0911 0.6207 225 G 0.2226 0.0687 0.7087 226 G 0.2376 0.0489 0.7135 227 I 0.1723 0.0593 0.7684 228 N 0.1367 0.0802 0.7831 229 N 0.1384 0.0733 0.7883 230 S 0.1805 0.0544 0.7651 231 L 0.1683 0.0246 0.8071 232 P 0.2009 0.0288 0.7703 233 N 0.1366 0.0305 0.8329 234 P 0.0707 0.0908 0.8386 235 H 0.0542 0.1585 0.7873 236 L 0.0500 0.2053 0.7446 237 R 0.1064 0.1363 0.7573 238 K 0.1602 0.1121 0.7277 239 D 0.0952 0.1776 0.7272 240 S 0.0760 0.1746 0.7494 241 N 0.0594 0.1799 0.7607 242 N 0.0623 0.1144 0.8233 243 P 0.0905 0.1565 0.7530 244 A 0.1209 0.2777 0.6013 245 L 0.0679 0.4469 0.4852 246 H 0.0638 0.5506 0.3856 247 F 0.0512 0.6228 0.3259 248 E 0.0554 0.6692 0.2754 249 W 0.0263 0.8544 0.1193 250 E 0.0347 0.8548 0.1105 251 I 0.0348 0.8611 0.1042 252 I 0.0425 0.8466 0.1109 253 H 0.0479 0.8111 0.1410 254 A 0.0531 0.7249 0.2220 255 F 0.0549 0.5307 0.4144 256 G 0.0469 0.3774 0.5757 257 K 0.0528 0.3283 0.6189 258 D 0.0723 0.2372 0.6905 259 A 0.1042 0.2437 0.6521 260 E 0.1262 0.1980 0.6758 261 G 0.0875 0.2368 0.6757 262 E 0.0696 0.2782 0.6522 263 R 0.0759 0.2921 0.6320 264 S 0.0713 0.3855 0.5432 265 S 0.0629 0.4945 0.4426 266 A 0.0604 0.5405 0.3992 267 I 0.0556 0.4952 0.4492 268 N 0.0506 0.3496 0.5998 269 T 0.0435 0.2824 0.6741 270 S 0.0519 0.2472 0.7009 271 P 0.0492 0.3301 0.6207 272 I 0.0568 0.3684 0.5748 273 S 0.0572 0.5381 0.4047 274 V 0.0569 0.6414 0.3017 275 V 0.0569 0.6477 0.2953 276 D 0.0370 0.6916 0.2714 277 K 0.0286 0.8498 0.1215 278 E 0.0288 0.8592 0.1120 279 R 0.0388 0.8381 0.1232 280 F 0.0467 0.7832 0.1701 281 S 0.0519 0.6712 0.2769 282 K 0.0521 0.4776 0.4704 283 Y 0.0679 0.2576 0.6745 284 H 0.0881 0.2021 0.7098 285 D 0.1027 0.1658 0.7315 286 N 0.1485 0.1166 0.7349 287 Y 0.2862 0.0792 0.6346 288 Y 0.2829 0.0402 0.6769 289 P 0.2936 0.0656 0.6408 290 G 0.5872 0.0634 0.3494 291 W 0.7516 0.0496 0.1987 292 Y 0.7867 0.0467 0.1666 293 L 0.7134 0.0578 0.2287 294 V 0.3845 0.0589 0.5566 295 D 0.1033 0.1070 0.7897 296 D 0.0337 0.3845 0.5818 297 T 0.0187 0.5910 0.3902 298 L 0.0197 0.7090 0.2713 299 E 0.0192 0.7206 0.2602 300 R 0.0195 0.7370 0.2435 301 A 0.0318 0.6988 0.2694 302 G 0.0386 0.5533 0.4081 303 R 0.0463 0.4892 0.4645 304 I 0.0789 0.4839 0.4372 305 K 0.0608 0.3464 0.5929 306 N 0.0356 0.0814 0.8830