# This file is the result of combining several RDB files, specifically # T0371.t06.dssp-ebghstl.rdb (weight 1.53986) # T0371.t06.stride-ebghtl.rdb (weight 1.24869) # T0371.t06.str2.rdb (weight 1.54758) # T0371.t06.alpha.rdb (weight 0.659012) # T0371.t04.dssp-ebghstl.rdb (weight 1.53986) # T0371.t04.stride-ebghtl.rdb (weight 1.24869) # T0371.t04.str2.rdb (weight 1.54758) # T0371.t04.alpha.rdb (weight 0.659012) # T0371.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0371.t2k.stride-ebghtl.rdb (weight 1.24869) # T0371.t2k.str2.rdb (weight 1.54758) # T0371.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 T0371.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0371 # Using neural net t06-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 T0371.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 4534 # # ============================================ # Comments from T0371.t06.stride-ebghtl.rdb # ============================================ # TARGET T0371 # Using neural net t06-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 T0371.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 4534 # # ============================================ # Comments from T0371.t06.str2.rdb # ============================================ # TARGET T0371 # Using neural net t06-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 T0371.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 4534 # # ============================================ # Comments from T0371.t06.alpha.rdb # ============================================ # TARGET T0371 # Using neural net t06-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 T0371.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 4534 # # ============================================ # Comments from T0371.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0371 # Using neural net t06-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 T0371.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 2160 # # ============================================ # Comments from T0371.t04.stride-ebghtl.rdb # ============================================ # TARGET T0371 # 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 T0371.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 2160 # # ============================================ # Comments from T0371.t04.str2.rdb # ============================================ # TARGET T0371 # Using neural net t04-2621-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 T0371.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 2160 # # ============================================ # Comments from T0371.t04.alpha.rdb # ============================================ # TARGET T0371 # 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 T0371.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 2160 # # ============================================ # Comments from T0371.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0371 # 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 T0371.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 728 # # ============================================ # Comments from T0371.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0371 # 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 T0371.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 728 # # ============================================ # Comments from T0371.t2k.str2.rdb # ============================================ # TARGET T0371 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0371.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 728 # # ============================================ # Comments from T0371.t2k.alpha.rdb # ============================================ # TARGET T0371 # 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 T0371.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 728 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0722 0.0366 0.8913 2 Q 0.0960 0.0718 0.8322 3 I 0.0167 0.8154 0.1680 4 E 0.0073 0.8473 0.1454 5 S 0.0108 0.8534 0.1357 6 F 0.0079 0.8897 0.1023 7 K 0.0080 0.8890 0.1031 8 S 0.0079 0.8799 0.1122 9 L 0.0086 0.8612 0.1302 10 L 0.0156 0.7825 0.2019 11 P 0.0093 0.5427 0.4479 12 K 0.0220 0.2549 0.7232 13 Y 0.1192 0.0256 0.8552 14 K 0.1671 0.0468 0.7861 15 C 0.9053 0.0042 0.0905 16 I 0.9311 0.0033 0.0656 17 F 0.9257 0.0038 0.0705 18 F 0.9050 0.0052 0.0898 19 D 0.5561 0.0056 0.4383 20 A 0.1055 0.0937 0.8008 21 F 0.0570 0.0538 0.8892 22 G 0.0978 0.0856 0.8166 23 V 0.4236 0.0524 0.5240 24 L 0.7394 0.0418 0.2188 25 K 0.6159 0.0654 0.3187 26 T 0.3343 0.0824 0.5833 27 Y 0.0854 0.1358 0.7789 28 N 0.0656 0.2022 0.7322 29 G 0.0613 0.3239 0.6149 30 L 0.0740 0.3627 0.5633 31 L 0.0447 0.4467 0.5085 32 P 0.0108 0.7753 0.2139 33 G 0.0121 0.7870 0.2009 34 I 0.0066 0.9038 0.0896 35 E 0.0055 0.9458 0.0487 36 N 0.0050 0.9537 0.0413 37 T 0.0047 0.9561 0.0392 38 F 0.0048 0.9542 0.0411 39 D 0.0048 0.9537 0.0415 40 Y 0.0049 0.9497 0.0453 41 L 0.0055 0.9378 0.0567 42 K 0.0076 0.9010 0.0914 43 A 0.0099 0.7798 0.2103 44 Q 0.0450 0.3409 0.6141 45 G 0.0378 0.0318 0.9304 46 Q 0.0870 0.0115 0.9015 47 D 0.4102 0.0098 0.5801 48 Y 0.8519 0.0062 0.1419 49 Y 0.9003 0.0062 0.0935 50 I 0.9077 0.0055 0.0869 51 V 0.8578 0.0106 0.1315 52 T 0.6068 0.0260 0.3673 53 N 0.1942 0.0474 0.7583 54 D 0.1136 0.0685 0.8179 55 A 0.0626 0.1427 0.7947 56 S 0.0820 0.1245 0.7934 57 R 0.1029 0.0840 0.8131 58 S 0.0731 0.0772 0.8498 59 P 0.0077 0.8814 0.1110 60 E 0.0054 0.9225 0.0721 61 Q 0.0051 0.9382 0.0567 62 L 0.0049 0.9470 0.0482 63 A 0.0050 0.9480 0.0470 64 D 0.0050 0.9435 0.0515 65 S 0.0050 0.9403 0.0547 66 Y 0.0057 0.9289 0.0654 67 H 0.0059 0.8997 0.0944 68 K 0.0092 0.7849 0.2059 69 L 0.0427 0.4316 0.5257 70 G 0.0424 0.1009 0.8566 71 L 0.0732 0.0793 0.8475 72 F 0.0945 0.1231 0.7824 73 S 0.1241 0.1095 0.7664 74 I 0.1478 0.0505 0.8017 75 T 0.1198 0.0455 0.8347 76 A 0.0158 0.7424 0.2418 77 D 0.0155 0.7452 0.2393 78 K 0.0393 0.7466 0.2141 79 I 0.1547 0.5214 0.3239 80 I 0.1734 0.4094 0.4172 81 S 0.1269 0.3568 0.5163 82 S 0.0333 0.5957 0.3709 83 G 0.0140 0.8041 0.1820 84 M 0.0087 0.9147 0.0766 85 I 0.0062 0.9358 0.0580 86 T 0.0051 0.9451 0.0497 87 K 0.0058 0.9461 0.0481 88 E 0.0059 0.9435 0.0507 89 Y 0.0060 0.9333 0.0607 90 I 0.0079 0.9032 0.0889 91 D 0.0113 0.8216 0.1671 92 L 0.0224 0.6285 0.3490 93 K 0.0569 0.3127 0.6304 94 V 0.0671 0.1493 0.7835 95 D 0.0503 0.1692 0.7805 96 G 0.0641 0.1120 0.8239 97 G 0.2119 0.0666 0.7215 98 I 0.6203 0.0236 0.3562 99 V 0.8246 0.0130 0.1625 100 A 0.8521 0.0129 0.1350 101 Y 0.8074 0.0165 0.1761 102 L 0.5238 0.0468 0.4294 103 G 0.1695 0.0517 0.7788 104 T 0.0716 0.2196 0.7088 105 A 0.0489 0.5123 0.4388 106 N 0.0416 0.6439 0.3145 107 S 0.0254 0.7748 0.1998 108 A 0.0139 0.8679 0.1183 109 N 0.0125 0.8969 0.0906 110 Y 0.0107 0.9136 0.0756 111 L 0.0117 0.9060 0.0822 112 V 0.0098 0.8966 0.0937 113 S 0.0113 0.8436 0.1451 114 D 0.0437 0.5187 0.4376 115 G 0.0480 0.1623 0.7896 116 I 0.1532 0.1598 0.6870 117 K 0.3394 0.1912 0.4694 118 M 0.3101 0.2283 0.4616 119 L 0.2419 0.1967 0.5614 120 P 0.1608 0.1662 0.6729 121 V 0.1003 0.2286 0.6710 122 S 0.0807 0.3781 0.5411 123 A 0.0802 0.4777 0.4420 124 I 0.0892 0.4779 0.4329 125 D 0.0885 0.4915 0.4200 126 D 0.0739 0.5260 0.4001 127 S 0.0758 0.4901 0.4341 128 N 0.0616 0.5024 0.4359 129 I 0.0474 0.5240 0.4285 130 G 0.0496 0.5177 0.4327 131 E 0.0634 0.5033 0.4333 132 V 0.0788 0.5608 0.3605 133 N 0.1114 0.6298 0.2588 134 A 0.1863 0.6230 0.1907 135 L 0.2905 0.5657 0.1439 136 V 0.3662 0.5021 0.1318 137 L 0.3647 0.4651 0.1703 138 L 0.2905 0.4210 0.2885 139 D 0.2028 0.3415 0.4557 140 D 0.1071 0.3315 0.5615 141 E 0.0704 0.3253 0.6043 142 G 0.0769 0.3335 0.5896 143 F 0.1185 0.2568 0.6246 144 N 0.1343 0.1981 0.6676 145 W 0.1171 0.1621 0.7208 146 F 0.0526 0.3850 0.5624 147 H 0.0084 0.8414 0.1502 148 D 0.0095 0.8580 0.1325 149 L 0.0064 0.9269 0.0667 150 N 0.0055 0.9489 0.0457 151 K 0.0047 0.9526 0.0427 152 T 0.0048 0.9541 0.0411 153 V 0.0048 0.9523 0.0429 154 N 0.0049 0.9496 0.0455 155 L 0.0050 0.9425 0.0525 156 L 0.0059 0.9273 0.0668 157 R 0.0086 0.8813 0.1101 158 K 0.0206 0.7131 0.2662 159 R 0.0423 0.2491 0.7086 160 T 0.0365 0.0293 0.9343 161 I 0.1062 0.0107 0.8831 162 P 0.5119 0.0107 0.4774 163 A 0.8965 0.0057 0.0978 164 I 0.9222 0.0039 0.0739 165 V 0.9149 0.0043 0.0808 166 A 0.8344 0.0108 0.1548 167 N 0.3490 0.0178 0.6332 168 T 0.0838 0.0932 0.8230 169 D 0.1082 0.0867 0.8051 170 N 0.1413 0.1608 0.6979 171 T 0.1969 0.1251 0.6780 172 Y 0.2817 0.1108 0.6075 173 P 0.3049 0.1162 0.5789 174 L 0.1729 0.1739 0.6532 175 T 0.1194 0.3177 0.5629 176 K 0.1044 0.2938 0.6018 177 T 0.0971 0.2520 0.6509 178 D 0.1585 0.1929 0.6486 179 V 0.2453 0.2048 0.5499 180 A 0.2090 0.2150 0.5759 181 I 0.1159 0.2897 0.5943 182 A 0.0760 0.2677 0.6563 183 I 0.0579 0.4930 0.4491 184 G 0.0500 0.5964 0.3536 185 G 0.0506 0.7199 0.2295 186 V 0.0176 0.8996 0.0828 187 A 0.0080 0.9420 0.0501 188 T 0.0082 0.9459 0.0459 189 M 0.0074 0.9459 0.0466 190 I 0.0094 0.9419 0.0487 191 E 0.0094 0.9354 0.0551 192 S 0.0128 0.8983 0.0889 193 I 0.0263 0.8209 0.1528 194 L 0.0707 0.6120 0.3172 195 G 0.0825 0.2808 0.6366 196 R 0.0890 0.1798 0.7312 197 R 0.1750 0.1372 0.6878 198 F 0.2925 0.1573 0.5502 199 I 0.3639 0.1566 0.4795 200 R 0.3578 0.1481 0.4941 201 F 0.2521 0.1245 0.6233 202 G 0.1396 0.0706 0.7898 203 K 0.1072 0.0584 0.8344 204 P 0.0836 0.0696 0.8468 205 D 0.0595 0.0811 0.8594 206 S 0.0097 0.8331 0.1572 207 Q 0.0062 0.9154 0.0784 208 M 0.0051 0.9381 0.0568 209 F 0.0047 0.9535 0.0418 210 M 0.0047 0.9552 0.0401 211 F 0.0047 0.9568 0.0384 212 A 0.0047 0.9578 0.0375 213 Y 0.0048 0.9559 0.0393 214 D 0.0049 0.9445 0.0506 215 M 0.0049 0.9260 0.0690 216 L 0.0065 0.8938 0.0997 217 R 0.0060 0.8685 0.1255 218 Q 0.0098 0.7696 0.2206 219 K 0.0428 0.4920 0.4652 220 M 0.0414 0.2789 0.6797 221 E 0.0470 0.0972 0.8558 222 I 0.0768 0.0371 0.8861 223 S 0.0749 0.0275 0.8977 224 K 0.0440 0.4690 0.4870 225 R 0.0460 0.4681 0.4859 226 E 0.2767 0.3498 0.3735 227 I 0.7920 0.0232 0.1848 228 L 0.8785 0.0116 0.1099 229 M 0.8914 0.0103 0.0983 230 V 0.7653 0.0455 0.1891 231 G 0.4492 0.0464 0.5045 232 D 0.1542 0.0737 0.7721 233 T 0.0805 0.0853 0.8343 234 L 0.0312 0.4964 0.4724 235 H 0.0200 0.6856 0.2944 236 T 0.0172 0.7946 0.1881 237 D 0.0154 0.8608 0.1238 238 I 0.0088 0.9208 0.0704 239 L 0.0069 0.9355 0.0576 240 G 0.0060 0.9382 0.0559 241 G 0.0061 0.9378 0.0562 242 N 0.0070 0.9160 0.0770 243 K 0.0117 0.7968 0.1915 244 F 0.0487 0.3462 0.6050 245 G 0.0623 0.0330 0.9047 246 L 0.1365 0.0185 0.8450 247 D 0.3521 0.0517 0.5962 248 T 0.8751 0.0138 0.1112 249 A 0.9112 0.0090 0.0798 250 L 0.9181 0.0062 0.0757 251 V 0.8733 0.0115 0.1151 252 L 0.5978 0.0234 0.3787 253 T 0.1580 0.0664 0.7756 254 G 0.0867 0.0586 0.8548 255 N 0.1680 0.0751 0.7569 256 T 0.1972 0.0656 0.7371 257 R 0.1295 0.1069 0.7637 258 I 0.0310 0.5744 0.3946 259 D 0.0261 0.6281 0.3459 260 D 0.0418 0.6201 0.3381 261 A 0.0612 0.4949 0.4439 262 E 0.0676 0.3695 0.5629 263 T 0.0698 0.2532 0.6770 264 K 0.0685 0.1731 0.7584 265 I 0.0901 0.1130 0.7969 266 K 0.1588 0.0714 0.7699 267 S 0.1240 0.0403 0.8357 268 T 0.1662 0.0478 0.7860 269 G 0.2820 0.0666 0.6514 270 I 0.7034 0.0264 0.2702 271 V 0.7932 0.0140 0.1927 272 P 0.6189 0.0227 0.3584 273 T 0.2395 0.0798 0.6807 274 H 0.1055 0.0461 0.8484 275 I 0.0216 0.7365 0.2419 276 C 0.0112 0.8040 0.1848 277 E 0.0130 0.8289 0.1581 278 S 0.0493 0.7670 0.1837 279 A 0.0874 0.5538 0.3588 280 V 0.1269 0.4286 0.4445 281 I 0.1954 0.3321 0.4725 282 E 0.2136 0.2261 0.5603 283 L 0.0705 0.0421 0.8874