# This file is the result of combining several RDB files, specifically # T0146.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0146.t2k.stride-ebghtl.rdb (weight 1.24869) # T0146.t2k.str.rdb (weight 1.53983) # T0146.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 T0146.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0146 # 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 T0146.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 50 # # ============================================ # Comments from T0146.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0146 # 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 T0146.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 50 # # ============================================ # Comments from T0146.t2k.str.rdb # ============================================ # TARGET T0146 # 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 T0146.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 50 # # ============================================ # Comments from T0146.t2k.alpha.rdb # ============================================ # TARGET T0146 # 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 T0146.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 50 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0763 0.0267 0.8970 2 F 0.2134 0.0512 0.7354 3 T 0.2284 0.0619 0.7096 4 P 0.1475 0.1009 0.7516 5 F 0.0877 0.1145 0.7978 6 P 0.0769 0.1164 0.8067 7 P 0.0791 0.2331 0.6877 8 R 0.0907 0.2771 0.6322 9 Q 0.1012 0.2916 0.6072 10 P 0.1057 0.3366 0.5577 11 T 0.1349 0.3065 0.5586 12 A 0.1268 0.4039 0.4693 13 S 0.1182 0.3875 0.4943 14 A 0.1101 0.3579 0.5320 15 R 0.1150 0.2537 0.6313 16 L 0.1156 0.1595 0.7249 17 P 0.1426 0.1071 0.7503 18 L 0.3692 0.0662 0.5646 19 T 0.6883 0.0447 0.2670 20 L 0.8355 0.0204 0.1441 21 M 0.8343 0.0124 0.1533 22 T 0.7429 0.0096 0.2475 23 L 0.2595 0.1416 0.5989 24 D 0.0596 0.2042 0.7362 25 D 0.0641 0.2109 0.7251 26 W 0.2148 0.0788 0.7064 27 A 0.5770 0.0415 0.3815 28 L 0.8793 0.0059 0.1148 29 A 0.9069 0.0064 0.0867 30 T 0.9100 0.0047 0.0853 31 I 0.8689 0.0091 0.1220 32 T 0.5806 0.0286 0.3909 33 G 0.2197 0.0365 0.7438 34 A 0.0390 0.3425 0.6185 35 D 0.0551 0.3843 0.5605 36 S 0.0079 0.8085 0.1836 37 E 0.0048 0.9056 0.0895 38 K 0.0057 0.9100 0.0843 39 Y 0.0058 0.9175 0.0767 40 M 0.0067 0.9090 0.0842 41 Q 0.0067 0.8631 0.1302 42 G 0.0073 0.7789 0.2138 43 Q 0.0171 0.7834 0.1995 44 V 0.0566 0.6657 0.2777 45 T 0.0500 0.5728 0.3772 46 A 0.0544 0.5038 0.4418 47 D 0.0770 0.4801 0.4429 48 V 0.0197 0.7723 0.2080 49 S 0.0175 0.7185 0.2640 50 Q 0.0243 0.5922 0.3835 51 M 0.0727 0.2766 0.6507 52 A 0.0670 0.1488 0.7841 53 E 0.0420 0.2318 0.7262 54 D 0.0487 0.1451 0.8062 55 Q 0.1997 0.1065 0.6938 56 H 0.5267 0.0444 0.4289 57 L 0.7143 0.0454 0.2404 58 L 0.7797 0.0465 0.1738 59 A 0.7983 0.0462 0.1555 60 A 0.8411 0.0298 0.1292 61 H 0.8409 0.0209 0.1382 62 C 0.7893 0.0149 0.1958 63 D 0.2032 0.0182 0.7787 64 A 0.0234 0.1266 0.8501 65 K 0.0505 0.0322 0.9172 66 G 0.1013 0.0495 0.8492 67 K 0.4200 0.0494 0.5305 68 M 0.7964 0.0382 0.1654 69 W 0.7685 0.0536 0.1779 70 S 0.7698 0.0496 0.1806 71 N 0.7961 0.0433 0.1607 72 L 0.8667 0.0236 0.1097 73 R 0.9029 0.0142 0.0829 74 L 0.9159 0.0083 0.0758 75 F 0.9027 0.0092 0.0882 76 R 0.8739 0.0098 0.1163 77 D 0.5970 0.0346 0.3684 78 G 0.0848 0.0584 0.8568 79 D 0.0439 0.0661 0.8901 80 G 0.4805 0.0256 0.4939 81 F 0.8520 0.0050 0.1430 82 A 0.9074 0.0045 0.0880 83 W 0.9134 0.0043 0.0823 84 I 0.8893 0.0046 0.1060 85 E 0.6293 0.0086 0.3621 86 R 0.1860 0.0147 0.7993 87 R 0.0093 0.5818 0.4089 88 S 0.0082 0.6128 0.3790 89 V 0.0122 0.6489 0.3389 90 R 0.0121 0.6945 0.2933 91 E 0.0076 0.8494 0.1431 92 P 0.0073 0.8911 0.1016 93 Q 0.0071 0.9164 0.0766 94 L 0.0048 0.9458 0.0494 95 T 0.0047 0.9482 0.0472 96 E 0.0047 0.9408 0.0544 97 L 0.0057 0.9349 0.0594 98 K 0.0055 0.9180 0.0765 99 K 0.0104 0.8300 0.1596 100 Y 0.0484 0.6706 0.2810 101 A 0.0934 0.5656 0.3411 102 V 0.1776 0.4193 0.4031 103 F 0.1531 0.3237 0.5232 104 S 0.1779 0.2016 0.6205 105 K 0.3621 0.0793 0.5585 106 V 0.6229 0.0219 0.3551 107 T 0.7472 0.0129 0.2399 108 I 0.7533 0.0155 0.2312 109 A 0.6067 0.0225 0.3708 110 P 0.4451 0.0374 0.5175 111 D 0.2040 0.0853 0.7107 112 D 0.1470 0.1655 0.6875 113 E 0.0588 0.5875 0.3537 114 R 0.1216 0.5823 0.2961 115 V 0.2662 0.5359 0.1979 116 L 0.3701 0.4939 0.1360 117 L 0.3616 0.5248 0.1137 118 G 0.3216 0.5617 0.1166 119 V 0.3014 0.5330 0.1657 120 A 0.2284 0.4598 0.3117 121 G 0.1599 0.2316 0.6085 122 F 0.0839 0.2451 0.6710 123 Q 0.0690 0.3694 0.5616 124 A 0.0211 0.7427 0.2362 125 R 0.0133 0.8220 0.1647 126 A 0.0131 0.8566 0.1304 127 A 0.0158 0.8449 0.1393 128 L 0.0187 0.8309 0.1504 129 A 0.0221 0.8245 0.1535 130 N 0.0214 0.7722 0.2064 131 L 0.0275 0.7075 0.2650 132 F 0.0545 0.5518 0.3937 133 S 0.0668 0.4505 0.4827 134 E 0.0682 0.3179 0.6139 135 L 0.0824 0.1637 0.7539 136 P 0.0645 0.1576 0.7779 137 S 0.0620 0.3023 0.6356 138 K 0.0519 0.4030 0.5451 139 E 0.0835 0.4129 0.5036 140 K 0.1889 0.3329 0.4782 141 Q 0.2448 0.3340 0.4212 142 V 0.2870 0.2828 0.4302 143 V 0.2219 0.2303 0.5477 144 K 0.1740 0.1159 0.7100 145 E 0.2021 0.0936 0.7043 146 G 0.2747 0.0725 0.6528 147 A 0.6373 0.0385 0.3242 148 T 0.8225 0.0196 0.1578 149 T 0.8360 0.0231 0.1409 150 L 0.8085 0.0224 0.1691 151 L 0.6651 0.0298 0.3051 152 W 0.3983 0.0340 0.5677 153 F 0.2159 0.1177 0.6665 154 E 0.1796 0.1219 0.6985 155 H 0.2188 0.0944 0.6867 156 P 0.1181 0.1127 0.7692 157 A 0.0889 0.1743 0.7368 158 E 0.0923 0.1621 0.7456 159 R 0.2001 0.0844 0.7155 160 F 0.5928 0.0265 0.3807 161 L 0.8001 0.0175 0.1823 162 I 0.8574 0.0152 0.1274 163 V 0.8219 0.0140 0.1642 164 T 0.6101 0.0126 0.3773 165 D 0.2547 0.0154 0.7299 166 E 0.0187 0.5359 0.4453 167 A 0.0102 0.5922 0.3976 168 T 0.0123 0.6798 0.3079 169 A 0.0077 0.8178 0.1744 170 N 0.0061 0.8716 0.1224 171 M 0.0071 0.8979 0.0949 172 L 0.0074 0.9046 0.0880 173 T 0.0077 0.9073 0.0851 174 D 0.0076 0.8877 0.1047 175 K 0.0082 0.8552 0.1366 176 L 0.0164 0.7937 0.1899 177 R 0.0250 0.6978 0.2772 178 G 0.0227 0.5710 0.4063 179 E 0.0280 0.4145 0.5575 180 A 0.0347 0.2458 0.7196 181 E 0.0448 0.2202 0.7349 182 L 0.0442 0.2379 0.7179 183 N 0.0465 0.1831 0.7704 184 N 0.0474 0.1305 0.8221 185 S 0.0183 0.7140 0.2677 186 Q 0.0087 0.8285 0.1628 187 Q 0.0055 0.9098 0.0847 188 W 0.0056 0.9271 0.0673 189 L 0.0056 0.9311 0.0634 190 A 0.0053 0.9395 0.0553 191 L 0.0082 0.9278 0.0641 192 N 0.0081 0.9205 0.0714 193 I 0.0102 0.9113 0.0786 194 E 0.0101 0.8970 0.0930 195 A 0.0423 0.6249 0.3329 196 G 0.0319 0.1672 0.8010 197 F 0.0806 0.1014 0.8180 198 P 0.1549 0.1184 0.7267 199 V 0.1898 0.2158 0.5944 200 I 0.1506 0.1997 0.6497 201 D 0.1171 0.2548 0.6281 202 A 0.1058 0.3789 0.5152 203 A 0.1066 0.3438 0.5496 204 N 0.1078 0.2548 0.6374 205 S 0.0608 0.2420 0.6972 206 G 0.0465 0.2250 0.7285 207 Q 0.1063 0.1991 0.6945 208 F 0.2272 0.1417 0.6311 209 I 0.2413 0.1381 0.6205 210 P 0.1551 0.4407 0.4042 211 Q 0.0807 0.6614 0.2578 212 A 0.1593 0.5893 0.2514 213 T 0.1405 0.5531 0.3065 214 N 0.1786 0.3475 0.4739 215 L 0.2268 0.3445 0.4288 216 Q 0.2330 0.4015 0.3655 217 A 0.2700 0.3698 0.3603 218 L 0.2408 0.2083 0.5509 219 G 0.2170 0.1115 0.6715 220 G 0.3905 0.0693 0.5402 221 I 0.5497 0.0409 0.4093 222 S 0.5862 0.0279 0.3859 223 F 0.4437 0.0795 0.4768 224 K 0.2514 0.0894 0.6592 225 K 0.1561 0.0973 0.7465 226 G 0.1317 0.0680 0.8003 227 C 0.1401 0.0836 0.7763 228 Y 0.1792 0.0816 0.7392 229 T 0.1292 0.1720 0.6988 230 G 0.0953 0.2626 0.6421 231 Q 0.0715 0.7519 0.1766 232 E 0.0816 0.8363 0.0822 233 M 0.0430 0.9057 0.0513 234 V 0.0469 0.9020 0.0512 235 A 0.0456 0.9044 0.0500 236 R 0.0365 0.9040 0.0595 237 A 0.0288 0.8920 0.0792 238 K 0.0299 0.8458 0.1244 239 F 0.0288 0.7046 0.2666 240 R 0.0524 0.2534 0.6941 241 G 0.0457 0.0534 0.9009 242 A 0.1196 0.0379 0.8425 243 N 0.2642 0.0449 0.6909 244 K 0.3395 0.1019 0.5586 245 R 0.4972 0.1045 0.3983 246 A 0.7172 0.0544 0.2284 247 L 0.8177 0.0232 0.1591 248 W 0.8289 0.0198 0.1513 249 L 0.8588 0.0146 0.1266 250 L 0.8402 0.0164 0.1434 251 A 0.7824 0.0195 0.1982 252 G 0.5772 0.0352 0.3876 253 S 0.2719 0.0634 0.6647 254 A 0.1150 0.0910 0.7939 255 S 0.0998 0.1107 0.7894 256 R 0.1436 0.0497 0.8067 257 L 0.1465 0.0274 0.8261 258 P 0.1117 0.0375 0.8508 259 E 0.1132 0.0572 0.8296 260 A 0.0794 0.1006 0.8200 261 G 0.0872 0.0661 0.8467 262 E 0.2724 0.0422 0.6854 263 D 0.6510 0.0339 0.3151 264 L 0.7439 0.0360 0.2201 265 E 0.7909 0.0279 0.1811 266 L 0.7223 0.0389 0.2388 267 K 0.6221 0.0506 0.3273 268 M 0.5148 0.0817 0.4034 269 G 0.2257 0.1081 0.6661 270 E 0.1304 0.1698 0.6998 271 N 0.0684 0.1219 0.8097 272 W 0.1129 0.0622 0.8249 273 R 0.3706 0.0262 0.6032 274 R 0.6619 0.0143 0.3238 275 T 0.8039 0.0183 0.1778 276 G 0.8267 0.0123 0.1611 277 T 0.9029 0.0054 0.0917 278 V 0.9076 0.0059 0.0865 279 L 0.8748 0.0109 0.1143 280 A 0.7771 0.0241 0.1988 281 A 0.5673 0.0520 0.3807 282 V 0.3822 0.0714 0.5464 283 K 0.1695 0.0729 0.7576 284 L 0.1125 0.0712 0.8163 285 E 0.0434 0.2626 0.6940 286 D 0.0503 0.3026 0.6472 287 G 0.0970 0.3750 0.5280 288 Q 0.1718 0.4450 0.3832 289 V 0.2990 0.5082 0.1929 290 V 0.3696 0.5099 0.1206 291 V 0.3690 0.5484 0.0826 292 Q 0.3360 0.5849 0.0792 293 V 0.3668 0.5424 0.0908 294 V 0.3658 0.4902 0.1440 295 M 0.3206 0.4142 0.2652 296 N 0.1671 0.4310 0.4018 297 N 0.0743 0.3921 0.5336 298 D 0.0778 0.2864 0.6359 299 M 0.0920 0.2203 0.6877 300 E 0.0760 0.1910 0.7330 301 P 0.0713 0.2018 0.7269 302 D 0.1094 0.0978 0.7928 303 S 0.3567 0.0458 0.5974 304 I 0.7514 0.0156 0.2330 305 F 0.8446 0.0146 0.1408 306 R 0.8497 0.0161 0.1341 307 V 0.7546 0.0240 0.2213 308 R 0.4593 0.0486 0.4921 309 D 0.2653 0.0550 0.6798 310 D 0.2441 0.0419 0.7139 311 A 0.2604 0.0487 0.6909 312 N 0.3882 0.0396 0.5722 313 T 0.7382 0.0190 0.2428 314 L 0.8285 0.0114 0.1601 315 H 0.7936 0.0108 0.1956 316 I 0.6505 0.0217 0.3278 317 E 0.4024 0.0413 0.5563 318 P 0.2592 0.0398 0.7011 319 L 0.1393 0.0206 0.8402 320 P 0.1832 0.0400 0.7768 321 Y 0.3082 0.0604 0.6314 322 S 0.2671 0.0688 0.6641 323 L 0.1464 0.1385 0.7150 324 E 0.0777 0.1152 0.8071 325 E 0.0371 0.0513 0.9116