# 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 379 # # ============================================ # 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 379 # # ============================================ # Comments from T0316.t2k.str2.rdb # ============================================ # TARGET T0316 # 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 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 379 # # ============================================ # 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 379 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0810 0.0341 0.8849 2 S 0.1334 0.0396 0.8270 3 D 0.0985 0.0739 0.8276 4 N 0.0312 0.1988 0.7701 5 S 0.0349 0.1722 0.7929 6 K 0.0785 0.0613 0.8602 7 T 0.1985 0.0181 0.7834 8 R 0.6872 0.0047 0.3082 9 V 0.9243 0.0032 0.0725 10 V 0.9319 0.0033 0.0648 11 V 0.9283 0.0035 0.0682 12 G 0.9082 0.0042 0.0875 13 M 0.7255 0.0228 0.2517 14 S 0.2603 0.0334 0.7063 15 G 0.1160 0.0754 0.8087 16 G 0.0585 0.2013 0.7402 17 V 0.0442 0.6165 0.3393 18 D 0.0173 0.7818 0.2009 19 S 0.0052 0.9137 0.0811 20 S 0.0048 0.9549 0.0403 21 V 0.0047 0.9596 0.0357 22 T 0.0047 0.9595 0.0358 23 A 0.0047 0.9601 0.0352 24 L 0.0047 0.9608 0.0345 25 L 0.0047 0.9602 0.0352 26 L 0.0047 0.9584 0.0369 27 K 0.0049 0.9501 0.0451 28 E 0.0056 0.9053 0.0891 29 Q 0.0400 0.4520 0.5081 30 G 0.0371 0.0407 0.9222 31 Y 0.1047 0.0239 0.8714 32 D 0.5004 0.0203 0.4793 33 V 0.7699 0.0083 0.2218 34 I 0.8163 0.0347 0.1491 35 G 0.8939 0.0098 0.0963 36 I 0.9119 0.0064 0.0816 37 F 0.9028 0.0067 0.0905 38 M 0.8705 0.0115 0.1180 39 K 0.7900 0.0278 0.1822 40 N 0.6623 0.0298 0.3079 41 W 0.4142 0.0592 0.5266 42 D 0.2669 0.0597 0.6735 43 D 0.1400 0.0973 0.7626 44 T 0.0782 0.1012 0.8207 45 D 0.0619 0.1059 0.8322 46 E 0.0640 0.0992 0.8368 47 N 0.0912 0.1119 0.7970 48 G 0.1154 0.0961 0.7886 49 V 0.2113 0.0966 0.6921 50 C 0.2678 0.0726 0.6597 51 T 0.1608 0.0834 0.7558 52 A 0.0861 0.2152 0.6987 53 T 0.0200 0.7000 0.2799 54 E 0.0187 0.6601 0.3211 55 D 0.0303 0.6527 0.3170 56 Y 0.0052 0.9392 0.0556 57 K 0.0049 0.9516 0.0435 58 D 0.0048 0.9552 0.0400 59 V 0.0047 0.9590 0.0363 60 V 0.0047 0.9604 0.0350 61 A 0.0047 0.9602 0.0351 62 V 0.0047 0.9593 0.0360 63 A 0.0047 0.9576 0.0377 64 D 0.0053 0.9463 0.0484 65 Q 0.0070 0.9073 0.0856 66 I 0.0473 0.4762 0.4765 67 G 0.0508 0.0148 0.9344 68 I 0.0718 0.0082 0.9201 69 P 0.1818 0.0139 0.8043 70 Y 0.6084 0.0092 0.3824 71 Y 0.8375 0.0064 0.1561 72 S 0.9110 0.0045 0.0846 73 V 0.8649 0.0095 0.1255 74 N 0.6322 0.0103 0.3575 75 F 0.0327 0.6196 0.3477 76 E 0.0101 0.7393 0.2506 77 K 0.0078 0.8759 0.1163 78 E 0.0084 0.8929 0.0987 79 Y 0.0121 0.8661 0.1218 80 W 0.0069 0.9029 0.0902 81 D 0.0077 0.9004 0.0919 82 R 0.0090 0.8486 0.1424 83 V 0.0143 0.8502 0.1355 84 F 0.0076 0.8995 0.0930 85 E 0.0056 0.9399 0.0545 86 Y 0.0047 0.9477 0.0476 87 F 0.0048 0.9508 0.0445 88 L 0.0048 0.9518 0.0434 89 A 0.0048 0.9530 0.0422 90 E 0.0055 0.9450 0.0495 91 Y 0.0085 0.9210 0.0704 92 R 0.0091 0.8558 0.1351 93 A 0.0338 0.5026 0.4636 94 G 0.0300 0.1399 0.8301 95 R 0.0732 0.0454 0.8814 96 T 0.0968 0.0258 0.8774 97 P 0.0677 0.0421 0.8902 98 N 0.0872 0.0377 0.8751 99 P 0.1135 0.1066 0.7799 100 D 0.2305 0.1418 0.6277 101 V 0.2160 0.2955 0.4885 102 M 0.1679 0.2882 0.5440 103 C 0.0814 0.3190 0.5996 104 N 0.0787 0.2463 0.6749 105 K 0.0645 0.4583 0.4772 106 E 0.1620 0.4930 0.3450 107 I 0.3162 0.3841 0.2996 108 K 0.2698 0.3696 0.3606 109 F 0.0273 0.8286 0.1441 110 K 0.0066 0.9328 0.0606 111 A 0.0054 0.9452 0.0493 112 F 0.0053 0.9497 0.0451 113 L 0.0055 0.9545 0.0399 114 D 0.0052 0.9530 0.0418 115 Y 0.0051 0.9513 0.0436 116 A 0.0052 0.9499 0.0449 117 I 0.0052 0.9412 0.0536 118 T 0.0061 0.8717 0.1222 119 L 0.0441 0.3860 0.5699 120 G 0.0485 0.0192 0.9323 121 A 0.0928 0.0090 0.8982 122 D 0.2179 0.0495 0.7326 123 Y 0.8973 0.0098 0.0929 124 V 0.9191 0.0055 0.0753 125 A 0.8954 0.0072 0.0974 126 T 0.7504 0.0188 0.2308 127 G 0.2721 0.0299 0.6980 128 H 0.2674 0.0786 0.6541 129 Y 0.5674 0.0830 0.3496 130 A 0.7715 0.0420 0.1865 131 R 0.8131 0.0307 0.1561 132 V 0.8349 0.0202 0.1449 133 A 0.7700 0.0194 0.2106 134 R 0.7125 0.0259 0.2616 135 D 0.2727 0.0615 0.6657 136 E 0.0626 0.1020 0.8354 137 D 0.0601 0.0532 0.8868 138 G 0.1144 0.0443 0.8412 139 T 0.5121 0.0184 0.4695 140 V 0.8386 0.0076 0.1537 141 H 0.8717 0.0104 0.1179 142 M 0.8885 0.0092 0.1023 143 L 0.8318 0.0228 0.1454 144 R 0.7891 0.0216 0.1893 145 G 0.6218 0.0370 0.3412 146 V 0.4047 0.0508 0.5446 147 D 0.2355 0.0484 0.7161 148 N 0.0373 0.2944 0.6682 149 G 0.0491 0.2552 0.6957 150 K 0.0840 0.2867 0.6293 151 D 0.1747 0.2152 0.6101 152 Q 0.2734 0.3337 0.3929 153 T 0.3539 0.3927 0.2533 154 Y 0.3182 0.4940 0.1877 155 F 0.2866 0.5169 0.1965 156 L 0.2210 0.4994 0.2795 157 S 0.1461 0.3910 0.4629 158 Q 0.1272 0.2686 0.6042 159 L 0.1605 0.0559 0.7836 160 S 0.0944 0.0422 0.8634 161 Q 0.0060 0.8841 0.1099 162 E 0.0055 0.8991 0.0954 163 Q 0.0068 0.8979 0.0953 164 L 0.0096 0.8929 0.0974 165 Q 0.0100 0.8405 0.1495 166 K 0.0141 0.7298 0.2561 167 T 0.0429 0.6030 0.3540 168 M 0.1060 0.3465 0.5475 169 F 0.1167 0.1225 0.7608 170 P 0.0966 0.1354 0.7680 171 L 0.0455 0.3835 0.5710 172 G 0.0395 0.3402 0.6203 173 H 0.0403 0.3709 0.5888 174 L 0.0794 0.1733 0.7472 175 E 0.0716 0.1462 0.7822 176 K 0.0373 0.5079 0.4548 177 P 0.0085 0.9024 0.0891 178 E 0.0064 0.9399 0.0537 179 V 0.0048 0.9552 0.0400 180 R 0.0048 0.9563 0.0388 181 R 0.0047 0.9605 0.0347 182 L 0.0047 0.9605 0.0348 183 A 0.0047 0.9587 0.0366 184 E 0.0050 0.9506 0.0444 185 E 0.0057 0.9148 0.0795 186 A 0.0418 0.3868 0.5714 187 G 0.0368 0.0242 0.9390 188 L 0.0702 0.0192 0.9107 189 S 0.2217 0.0500 0.7282 190 T 0.2942 0.1541 0.5517 191 A 0.2843 0.1400 0.5757 192 K 0.2311 0.0695 0.6994 193 K 0.1876 0.0438 0.7687 194 K 0.1429 0.1229 0.7342 195 D 0.1402 0.1119 0.7479 196 S 0.1680 0.1283 0.7038 197 T 0.1432 0.0841 0.7727 198 G 0.1792 0.0668 0.7540 199 I 0.4442 0.0521 0.5037 200 C 0.5158 0.0529 0.4312 201 F 0.5701 0.0448 0.3851 202 I 0.3706 0.0382 0.5912 203 G 0.1564 0.0368 0.8067 204 E 0.0691 0.1218 0.8092 205 K 0.0647 0.1641 0.7712 206 N 0.1041 0.2003 0.6956 207 F 0.0115 0.8474 0.1411 208 K 0.0058 0.9273 0.0669 209 N 0.0056 0.9404 0.0540 210 F 0.0067 0.9373 0.0560 211 L 0.0076 0.9118 0.0807 212 S 0.0117 0.8247 0.1636 213 N 0.0156 0.7475 0.2370 214 Y 0.0435 0.5311 0.4253 215 L 0.0649 0.1262 0.8089 216 P 0.0666 0.0602 0.8731 217 A 0.0946 0.0767 0.8287 218 Q 0.1130 0.0385 0.8485 219 P 0.1890 0.0566 0.7544 220 G 0.3145 0.0365 0.6490 221 R 0.6091 0.0141 0.3768 222 M 0.7569 0.0070 0.2362 223 M 0.8318 0.0051 0.1632 224 T 0.3852 0.0096 0.6052 225 V 0.0620 0.1103 0.8278 226 D 0.0496 0.0180 0.9324 227 G 0.0592 0.0284 0.9124 228 R 0.3978 0.0085 0.5937 229 D 0.8894 0.0033 0.1073 230 M 0.8481 0.0168 0.1351 231 G 0.8191 0.0141 0.1669 232 E 0.7265 0.0359 0.2376 233 H 0.6516 0.0338 0.3147 234 A 0.4405 0.0618 0.4977 235 G 0.3639 0.0592 0.5770 236 L 0.6128 0.0514 0.3358 237 M 0.6668 0.0616 0.2716 238 Y 0.7244 0.0609 0.2146 239 Y 0.6816 0.0579 0.2605 240 T 0.5880 0.0550 0.3570 241 I 0.4442 0.1840 0.3718 242 G 0.3172 0.2126 0.4702 243 Q 0.3380 0.2475 0.4144 244 R 0.3553 0.2392 0.4055 245 G 0.1464 0.2153 0.6383 246 G 0.1150 0.1201 0.7649 247 L 0.2299 0.0858 0.6843 248 G 0.2896 0.0523 0.6581 249 I 0.2727 0.0950 0.6322 250 G 0.1967 0.1279 0.6754 251 G 0.1498 0.1126 0.7376 252 Q 0.1615 0.0960 0.7425 253 H 0.1108 0.1141 0.7750 254 G 0.0683 0.1146 0.8172 255 G 0.0612 0.0924 0.8464 256 D 0.0943 0.0812 0.8244 257 N 0.1131 0.0518 0.8351 258 A 0.1873 0.0202 0.7924 259 P 0.3755 0.0120 0.6125 260 W 0.7713 0.0137 0.2150 261 F 0.8854 0.0058 0.1088 262 R 0.9173 0.0036 0.0791 263 Y 0.8764 0.0217 0.1019 264 R 0.8984 0.0066 0.0951 265 Q 0.7958 0.0111 0.1931 266 P 0.5622 0.0095 0.4284 267 D 0.0607 0.2667 0.6726 268 S 0.0360 0.2222 0.7418 269 K 0.0755 0.1549 0.7696 270 V 0.1466 0.0279 0.8255 271 T 0.8145 0.0057 0.1798 272 V 0.9245 0.0034 0.0721 273 H 0.9247 0.0033 0.0720 274 V 0.8725 0.0106 0.1169 275 K 0.6085 0.0080 0.3835 276 G 0.1832 0.0515 0.7653 277 E 0.0385 0.2934 0.6680 278 K 0.0261 0.4430 0.5309 279 T 0.0370 0.4165 0.5465 280 E 0.0789 0.3207 0.6004 281 V 0.0376 0.5428 0.4197 282 I 0.0578 0.5765 0.3657 283 F 0.1037 0.5576 0.3387 284 A 0.2083 0.4188 0.3729 285 E 0.2597 0.3317 0.4086 286 P 0.2805 0.3154 0.4041 287 Q 0.4575 0.1985 0.3440 288 R 0.6078 0.1184 0.2738 289 A 0.6658 0.0873 0.2469 290 I 0.5326 0.1221 0.3453 291 T 0.4053 0.1357 0.4590 292 P 0.3594 0.1391 0.5015 293 G 0.4474 0.1081 0.4445 294 Q 0.5567 0.0735 0.3698 295 A 0.5533 0.1046 0.3421 296 V 0.4585 0.0991 0.4424 297 V 0.3029 0.0900 0.6071 298 F 0.1709 0.0799 0.7491 299 Y 0.1242 0.0610 0.8148 300 D 0.0917 0.0550 0.8534 301 G 0.0724 0.1116 0.8161 302 E 0.0696 0.1275 0.8029 303 E 0.1074 0.0809 0.8116 304 C 0.2404 0.0550 0.7046 305 L 0.5787 0.0291 0.3922 306 G 0.8233 0.0091 0.1675 307 G 0.8830 0.0060 0.1110 308 G 0.9166 0.0035 0.0799 309 L 0.9189 0.0034 0.0777 310 I 0.9169 0.0035 0.0796 311 D 0.9072 0.0042 0.0886 312 N 0.8423 0.0134 0.1443 313 A 0.7392 0.0213 0.2395 314 Y 0.4354 0.0569 0.5077 315 R 0.1972 0.0389 0.7639 316 D 0.1152 0.0519 0.8329 317 G 0.1157 0.0516 0.8328 318 Q 0.2315 0.0215 0.7470 319 V 0.3364 0.0170 0.6466 320 C 0.6496 0.0112 0.3392 321 Q 0.8102 0.0062 0.1836 322 Y 0.7134 0.0055 0.2811 323 I 0.1086 0.0081 0.8833