# This file is the result of combining several RDB files, specifically # T0316.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0316.t2k.stride-ebghtl.rdb (weight 1.24869) # T0316.t2k.str2.rdb (weight 1.54758) # T0316.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 T0316.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 384 # # ============================================ # Comments from T0316.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 384 # # ============================================ # Comments from T0316.t2k.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 36.816 # # ============================================ # Comments from T0316.t2k.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 384 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1167 0.0497 0.8337 2 S 0.1451 0.0427 0.8122 3 D 0.0911 0.0898 0.8191 4 N 0.0449 0.1986 0.7565 5 S 0.0338 0.1870 0.7792 6 K 0.0868 0.0602 0.8530 7 T 0.2999 0.0177 0.6824 8 R 0.7468 0.0046 0.2486 9 V 0.9207 0.0032 0.0760 10 V 0.9319 0.0033 0.0648 11 V 0.9286 0.0035 0.0679 12 G 0.9060 0.0044 0.0897 13 M 0.7312 0.0220 0.2468 14 S 0.3207 0.0270 0.6523 15 G 0.1041 0.0617 0.8342 16 G 0.0970 0.1554 0.7475 17 V 0.0593 0.6201 0.3205 18 D 0.0159 0.8338 0.1503 19 S 0.0051 0.9423 0.0526 20 S 0.0048 0.9568 0.0384 21 V 0.0047 0.9603 0.0351 22 T 0.0047 0.9601 0.0352 23 A 0.0047 0.9601 0.0352 24 L 0.0047 0.9611 0.0342 25 L 0.0047 0.9605 0.0349 26 L 0.0047 0.9587 0.0366 27 K 0.0049 0.9526 0.0426 28 E 0.0057 0.9252 0.0692 29 Q 0.0399 0.4874 0.4727 30 G 0.0364 0.0400 0.9236 31 Y 0.0864 0.0205 0.8931 32 D 0.4245 0.0195 0.5559 33 V 0.8004 0.0086 0.1909 34 I 0.8087 0.0363 0.1551 35 G 0.8682 0.0158 0.1160 36 I 0.9017 0.0092 0.0891 37 F 0.8712 0.0192 0.1095 38 M 0.7552 0.0445 0.2003 39 K 0.6418 0.0516 0.3067 40 N 0.4962 0.0463 0.4575 41 W 0.3386 0.0628 0.5986 42 D 0.2229 0.0665 0.7106 43 D 0.1285 0.1090 0.7625 44 T 0.0703 0.1305 0.7992 45 D 0.0617 0.1515 0.7868 46 E 0.0623 0.1334 0.8043 47 N 0.0778 0.0969 0.8253 48 G 0.1011 0.0668 0.8321 49 V 0.2184 0.0596 0.7220 50 C 0.3561 0.0541 0.5898 51 T 0.1798 0.0771 0.7432 52 A 0.0986 0.1909 0.7105 53 T 0.0281 0.5799 0.3920 54 E 0.0215 0.5876 0.3909 55 D 0.0351 0.5766 0.3882 56 Y 0.0076 0.9015 0.0909 57 K 0.0049 0.9427 0.0524 58 D 0.0048 0.9508 0.0444 59 V 0.0047 0.9591 0.0362 60 V 0.0047 0.9604 0.0349 61 A 0.0047 0.9603 0.0350 62 V 0.0047 0.9595 0.0358 63 A 0.0047 0.9576 0.0377 64 D 0.0053 0.9438 0.0509 65 Q 0.0071 0.8951 0.0978 66 I 0.0473 0.5272 0.4254 67 G 0.0510 0.0174 0.9316 68 I 0.0691 0.0082 0.9227 69 P 0.1728 0.0144 0.8128 70 Y 0.7417 0.0086 0.2497 71 Y 0.9002 0.0066 0.0933 72 S 0.9187 0.0045 0.0768 73 V 0.8659 0.0107 0.1234 74 N 0.6240 0.0132 0.3627 75 F 0.0726 0.4238 0.5036 76 E 0.0174 0.6904 0.2922 77 K 0.0088 0.8653 0.1259 78 E 0.0092 0.8840 0.1067 79 Y 0.0131 0.8604 0.1266 80 W 0.0069 0.9031 0.0900 81 D 0.0078 0.9046 0.0876 82 R 0.0090 0.8774 0.1137 83 V 0.0134 0.8811 0.1055 84 F 0.0079 0.9022 0.0899 85 E 0.0058 0.9416 0.0526 86 Y 0.0047 0.9481 0.0471 87 F 0.0048 0.9501 0.0451 88 L 0.0048 0.9523 0.0429 89 A 0.0049 0.9546 0.0405 90 E 0.0056 0.9507 0.0438 91 Y 0.0088 0.9354 0.0558 92 R 0.0086 0.8961 0.0953 93 A 0.0337 0.5205 0.4458 94 G 0.0290 0.1532 0.8178 95 R 0.0651 0.0423 0.8925 96 T 0.0787 0.0243 0.8970 97 P 0.0743 0.0400 0.8857 98 N 0.0968 0.0407 0.8625 99 P 0.1096 0.1319 0.7584 100 D 0.2233 0.1850 0.5916 101 V 0.3047 0.2681 0.4273 102 M 0.2755 0.2487 0.4758 103 C 0.1540 0.2809 0.5651 104 N 0.0837 0.2083 0.7080 105 K 0.0543 0.3751 0.5706 106 E 0.1725 0.3830 0.4445 107 I 0.3339 0.3168 0.3492 108 K 0.2963 0.3272 0.3765 109 F 0.0271 0.8454 0.1275 110 K 0.0066 0.9282 0.0652 111 A 0.0064 0.9286 0.0650 112 F 0.0058 0.9434 0.0508 113 L 0.0055 0.9513 0.0432 114 D 0.0051 0.9536 0.0413 115 Y 0.0051 0.9508 0.0441 116 A 0.0051 0.9471 0.0478 117 I 0.0052 0.9375 0.0573 118 T 0.0061 0.8957 0.0983 119 L 0.0443 0.4731 0.4826 120 G 0.0507 0.0261 0.9232 121 A 0.1028 0.0115 0.8857 122 D 0.2567 0.0522 0.6912 123 Y 0.8958 0.0094 0.0948 124 V 0.9172 0.0055 0.0772 125 A 0.8898 0.0067 0.1035 126 T 0.7185 0.0185 0.2630 127 G 0.3773 0.0312 0.5915 128 H 0.3487 0.0841 0.5672 129 Y 0.5504 0.1119 0.3377 130 A 0.7017 0.1078 0.1905 131 R 0.7762 0.0554 0.1684 132 V 0.8234 0.0227 0.1539 133 A 0.7767 0.0153 0.2079 134 R 0.7137 0.0235 0.2628 135 D 0.2539 0.0452 0.7009 136 E 0.0450 0.0859 0.8691 137 D 0.0527 0.0411 0.9062 138 G 0.0845 0.0380 0.8775 139 T 0.4104 0.0174 0.5722 140 V 0.8299 0.0086 0.1615 141 H 0.8710 0.0127 0.1163 142 M 0.8903 0.0111 0.0986 143 L 0.8361 0.0247 0.1393 144 R 0.8013 0.0199 0.1788 145 G 0.6450 0.0345 0.3205 146 V 0.4052 0.0471 0.5478 147 D 0.2064 0.0421 0.7515 148 N 0.0291 0.2070 0.7640 149 G 0.0391 0.1756 0.7852 150 K 0.0694 0.2416 0.6889 151 D 0.1813 0.2146 0.6042 152 Q 0.2725 0.3838 0.3438 153 T 0.3987 0.3996 0.2018 154 Y 0.3718 0.4796 0.1485 155 F 0.2880 0.5358 0.1762 156 L 0.1958 0.5425 0.2617 157 S 0.1153 0.4819 0.4028 158 Q 0.0938 0.3743 0.5320 159 L 0.1375 0.1242 0.7383 160 S 0.0875 0.0810 0.8315 161 Q 0.0063 0.8765 0.1172 162 E 0.0057 0.8985 0.0957 163 Q 0.0067 0.8945 0.0988 164 L 0.0100 0.8928 0.0972 165 Q 0.0101 0.8499 0.1400 166 K 0.0131 0.7726 0.2143 167 T 0.0430 0.6358 0.3212 168 M 0.0908 0.3858 0.5234 169 F 0.0942 0.1834 0.7223 170 P 0.0789 0.1757 0.7454 171 L 0.0458 0.3169 0.6373 172 G 0.0370 0.2582 0.7048 173 H 0.0361 0.2881 0.6758 174 L 0.0770 0.1757 0.7474 175 E 0.0721 0.1469 0.7809 176 K 0.0398 0.5272 0.4330 177 P 0.0084 0.8526 0.1391 178 E 0.0073 0.9241 0.0686 179 V 0.0052 0.9503 0.0445 180 R 0.0049 0.9568 0.0383 181 R 0.0048 0.9604 0.0348 182 L 0.0047 0.9605 0.0348 183 A 0.0047 0.9591 0.0362 184 E 0.0049 0.9533 0.0418 185 E 0.0056 0.9333 0.0612 186 A 0.0418 0.5355 0.4228 187 G 0.0352 0.0304 0.9344 188 L 0.0663 0.0237 0.9100 189 S 0.1877 0.0746 0.7378 190 T 0.2827 0.2142 0.5031 191 A 0.3388 0.1812 0.4800 192 K 0.2989 0.0890 0.6121 193 K 0.2197 0.0621 0.7182 194 K 0.1292 0.1542 0.7166 195 D 0.1346 0.1185 0.7469 196 S 0.2212 0.1144 0.6644 197 T 0.2177 0.0781 0.7041 198 G 0.3231 0.0611 0.6159 199 I 0.6534 0.0339 0.3127 200 C 0.7126 0.0266 0.2608 201 F 0.7269 0.0194 0.2536 202 I 0.5329 0.0246 0.4425 203 G 0.2124 0.0293 0.7583 204 E 0.0800 0.1293 0.7907 205 K 0.0549 0.1768 0.7683 206 N 0.1013 0.2197 0.6790 207 F 0.0223 0.8180 0.1597 208 K 0.0080 0.9012 0.0909 209 N 0.0093 0.8973 0.0934 210 F 0.0182 0.8872 0.0946 211 L 0.0154 0.8627 0.1219 212 S 0.0090 0.7882 0.2028 213 N 0.0165 0.6655 0.3180 214 Y 0.0428 0.4544 0.5027 215 L 0.0647 0.0948 0.8406 216 P 0.0730 0.0406 0.8864 217 A 0.0987 0.0579 0.8434 218 Q 0.1104 0.0345 0.8551 219 P 0.2038 0.0419 0.7544 220 G 0.3405 0.0269 0.6326 221 R 0.6525 0.0083 0.3392 222 M 0.8177 0.0053 0.1770 223 M 0.8354 0.0051 0.1595 224 T 0.4814 0.0109 0.5077 225 V 0.1230 0.1069 0.7701 226 D 0.0531 0.0174 0.9295 227 G 0.0586 0.0286 0.9128 228 R 0.4448 0.0081 0.5471 229 D 0.8780 0.0032 0.1188 230 M 0.8265 0.0182 0.1553 231 G 0.8162 0.0142 0.1696 232 E 0.6788 0.0316 0.2897 233 H 0.5389 0.0404 0.4206 234 A 0.3165 0.0702 0.6132 235 G 0.4041 0.0663 0.5296 236 L 0.6474 0.0558 0.2968 237 M 0.7137 0.0617 0.2246 238 Y 0.7441 0.0596 0.1963 239 Y 0.6933 0.0562 0.2505 240 T 0.5932 0.0659 0.3410 241 I 0.4518 0.2022 0.3461 242 G 0.3605 0.2132 0.4263 243 Q 0.3168 0.2681 0.4151 244 R 0.2936 0.2668 0.4396 245 G 0.1661 0.2538 0.5801 246 G 0.1403 0.1411 0.7186 247 L 0.2026 0.0956 0.7019 248 G 0.2659 0.0627 0.6713 249 I 0.2655 0.1072 0.6274 250 G 0.1880 0.1261 0.6859 251 G 0.1466 0.1031 0.7504 252 Q 0.1213 0.1224 0.7563 253 H 0.0860 0.1345 0.7795 254 G 0.0617 0.1457 0.7926 255 G 0.0660 0.1358 0.7982 256 D 0.1031 0.1086 0.7882 257 N 0.1436 0.0622 0.7942 258 A 0.2085 0.0223 0.7692 259 P 0.4028 0.0175 0.5797 260 W 0.7676 0.0192 0.2132 261 F 0.8840 0.0081 0.1079 262 V 0.9020 0.0057 0.0923 263 V 0.8344 0.0256 0.1399 264 G 0.8317 0.0097 0.1586 265 K 0.6846 0.0159 0.2995 266 D 0.4955 0.0250 0.4794 267 L 0.0967 0.2998 0.6035 268 S 0.0704 0.2447 0.6848 269 K 0.1027 0.1904 0.7068 270 N 0.1905 0.0341 0.7754 271 I 0.7878 0.0068 0.2054 272 L 0.9224 0.0034 0.0743 273 Y 0.9227 0.0033 0.0740 274 V 0.8716 0.0102 0.1182 275 G 0.5640 0.0080 0.4280 276 Q 0.1655 0.0438 0.7907 277 G 0.0330 0.2196 0.7473 278 F 0.0265 0.3685 0.6050 279 Y 0.0397 0.3351 0.6253 280 H 0.0682 0.2853 0.6465 281 D 0.0235 0.5178 0.4587 282 S 0.0393 0.5720 0.3887 283 L 0.0852 0.5414 0.3733 284 M 0.1833 0.3941 0.4226 285 S 0.2231 0.3266 0.4503 286 T 0.2025 0.3380 0.4594 287 S 0.3729 0.2221 0.4050 288 L 0.5189 0.1473 0.3338 289 E 0.5738 0.1139 0.3123 290 A 0.4231 0.1883 0.3886 291 S 0.2196 0.2395 0.5409 292 Q 0.2299 0.2115 0.5587 293 V 0.3987 0.1301 0.4712 294 H 0.4716 0.0995 0.4289 295 F 0.4519 0.1282 0.4199 296 T 0.3996 0.1120 0.4885 297 R 0.2843 0.1009 0.6148 298 E 0.1871 0.0769 0.7361 299 M 0.1359 0.0526 0.8115 300 P 0.0909 0.0593 0.8498 301 E 0.0679 0.1401 0.7921 302 E 0.0589 0.1323 0.8088 303 F 0.1231 0.0564 0.8204 304 T 0.2818 0.0378 0.6804 305 L 0.6061 0.0169 0.3769 306 E 0.8333 0.0051 0.1616 307 C 0.8924 0.0037 0.1039 308 T 0.9189 0.0032 0.0779 309 A 0.9222 0.0033 0.0745 310 K 0.9184 0.0035 0.0781 311 F 0.9030 0.0033 0.0937 312 R 0.8155 0.0104 0.1742 313 Y 0.6849 0.0140 0.3010 314 R 0.3346 0.0335 0.6319 315 Q 0.1335 0.0274 0.8391 316 P 0.1028 0.0390 0.8582 317 D 0.1272 0.0393 0.8335 318 S 0.2464 0.0143 0.7393 319 K 0.5574 0.0085 0.4341 320 V 0.8455 0.0053 0.1492 321 T 0.9202 0.0033 0.0765 322 V 0.9213 0.0033 0.0755 323 H 0.9119 0.0043 0.0838 324 V 0.8736 0.0076 0.1188 325 K 0.5512 0.0237 0.4251 326 G 0.0610 0.0435 0.8954 327 E 0.0717 0.0667 0.8616 328 K 0.5905 0.0212 0.3883 329 T 0.8920 0.0036 0.1045 330 E 0.9222 0.0035 0.0743 331 V 0.9269 0.0031 0.0700 332 I 0.8855 0.0069 0.1076 333 F 0.7496 0.0074 0.2430 334 A 0.3326 0.0416 0.6258 335 E 0.1759 0.0216 0.8025 336 P 0.2031 0.0612 0.7358 337 Q 0.4368 0.0650 0.4982 338 R 0.6397 0.0566 0.3037 339 A 0.6709 0.0334 0.2958 340 I 0.5745 0.0230 0.4025 341 T 0.2486 0.0225 0.7289 342 P 0.0629 0.0661 0.8711 343 G 0.0805 0.0312 0.8883 344 Q 0.5124 0.0116 0.4760 345 A 0.8561 0.0042 0.1397 346 V 0.9192 0.0035 0.0772 347 V 0.9253 0.0035 0.0712 348 F 0.9190 0.0039 0.0771 349 Y 0.8702 0.0079 0.1219 350 D 0.3481 0.0313 0.6206 351 G 0.0456 0.0504 0.9040 352 E 0.1673 0.0664 0.7662 353 E 0.7599 0.0203 0.2199 354 C 0.8245 0.0253 0.1502 355 L 0.7443 0.0466 0.2091 356 G 0.5405 0.0688 0.3907 357 G 0.3887 0.1682 0.4431 358 G 0.4506 0.2325 0.3170 359 L 0.4882 0.3079 0.2039 360 I 0.3856 0.4488 0.1657 361 D 0.3421 0.4514 0.2065 362 N 0.3839 0.3914 0.2248 363 A 0.3755 0.3603 0.2642 364 Y 0.4407 0.2333 0.3260 365 R 0.2770 0.2123 0.5107 366 D 0.0611 0.1077 0.8312 367 G 0.0400 0.0654 0.8946 368 Q 0.3042 0.0569 0.6389 369 V 0.6380 0.0447 0.3173 370 C 0.6844 0.0485 0.2671 371 Q 0.6906 0.0481 0.2613 372 Y 0.5807 0.0502 0.3692 373 I 0.1447 0.0282 0.8271