# This file is the result of combining several RDB files, specifically # T0372.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0372.t2k.stride-ebghtl.rdb (weight 1.24869) # T0372.t2k.str2.rdb (weight 1.54758) # T0372.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 T0372.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0372 # 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 T0372.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 35 # # ============================================ # Comments from T0372.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0372 # 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 T0372.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 35 # # ============================================ # Comments from T0372.t2k.str2.rdb # ============================================ # TARGET T0372 # 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 T0372.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 35 # # ============================================ # Comments from T0372.t2k.alpha.rdb # ============================================ # TARGET T0372 # 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 T0372.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 35 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0646 0.0280 0.9074 2 I 0.1125 0.0288 0.8586 3 P 0.1357 0.0577 0.8066 4 F 0.1669 0.0427 0.7904 5 K 0.2351 0.0255 0.7395 6 D 0.3687 0.0157 0.6156 7 I 0.3347 0.0151 0.6502 8 T 0.1895 0.0147 0.7958 9 L 0.0594 0.5438 0.3968 10 A 0.0255 0.5775 0.3970 11 D 0.0326 0.6153 0.3521 12 R 0.0104 0.8598 0.1298 13 D 0.0077 0.8827 0.1096 14 T 0.0104 0.8730 0.1167 15 I 0.0132 0.8953 0.0915 16 T 0.0112 0.9123 0.0765 17 A 0.0114 0.9018 0.0867 18 F 0.0111 0.8778 0.1111 19 T 0.0227 0.8063 0.1710 20 M 0.0190 0.6805 0.3005 21 K 0.0260 0.4374 0.5367 22 S 0.0791 0.1643 0.7565 23 D 0.1057 0.0861 0.8081 24 R 0.1729 0.1460 0.6812 25 R 0.2129 0.1659 0.6211 26 N 0.2258 0.2006 0.5737 27 C 0.1902 0.2080 0.6018 28 D 0.1039 0.3311 0.5650 29 L 0.1237 0.3562 0.5201 30 S 0.2082 0.3367 0.4551 31 F 0.1201 0.7214 0.1585 32 S 0.0985 0.7724 0.1291 33 N 0.1016 0.7658 0.1327 34 L 0.1346 0.7495 0.1159 35 C 0.2530 0.6144 0.1326 36 S 0.2570 0.5785 0.1645 37 W 0.2087 0.5949 0.1964 38 R 0.1977 0.5235 0.2788 39 F 0.1555 0.4139 0.4307 40 L 0.1446 0.2964 0.5590 41 Y 0.1494 0.1596 0.6910 42 D 0.1979 0.0706 0.7315 43 T 0.5100 0.0399 0.4501 44 Q 0.7984 0.0165 0.1851 45 F 0.9024 0.0069 0.0907 46 A 0.9102 0.0058 0.0840 47 V 0.9115 0.0064 0.0821 48 I 0.8370 0.0209 0.1421 49 D 0.3661 0.0465 0.5874 50 D 0.1861 0.0668 0.7471 51 F 0.7731 0.0120 0.2150 52 L 0.9180 0.0035 0.0786 53 V 0.9288 0.0035 0.0677 54 F 0.9298 0.0033 0.0669 55 K 0.9178 0.0047 0.0775 56 F 0.8971 0.0052 0.0976 57 W 0.8267 0.0124 0.1610 58 A 0.5938 0.0297 0.3765 59 G 0.0972 0.0603 0.8424 60 E 0.0946 0.0488 0.8566 61 Q 0.4583 0.0214 0.5202 62 L 0.7104 0.0130 0.2767 63 A 0.7971 0.0143 0.1886 64 Y 0.7941 0.0184 0.1875 65 M 0.6704 0.0227 0.3069 66 M 0.4732 0.0213 0.5056 67 P 0.2415 0.0269 0.7316 68 V 0.1478 0.0626 0.7896 69 G 0.0870 0.0840 0.8290 70 N 0.0538 0.1053 0.8409 71 G 0.0480 0.1090 0.8430 72 D 0.0790 0.1168 0.8042 73 L 0.0299 0.6299 0.3402 74 K 0.0192 0.7701 0.2107 75 A 0.0132 0.8396 0.1472 76 V 0.0113 0.8859 0.1028 77 L 0.0060 0.9349 0.0591 78 R 0.0052 0.9484 0.0464 79 K 0.0048 0.9519 0.0433 80 L 0.0048 0.9508 0.0444 81 I 0.0052 0.9453 0.0495 82 E 0.0059 0.9220 0.0720 83 D 0.0070 0.8936 0.0994 84 A 0.0110 0.8571 0.1319 85 D 0.0106 0.8443 0.1450 86 K 0.0150 0.7717 0.2134 87 E 0.0320 0.6068 0.3612 88 K 0.0410 0.4579 0.5011 89 H 0.0562 0.2749 0.6690 90 N 0.0636 0.1948 0.7416 91 F 0.1426 0.2223 0.6351 92 C 0.3024 0.1982 0.4994 93 M 0.4343 0.1828 0.3828 94 L 0.4548 0.1888 0.3564 95 G 0.4307 0.1657 0.4036 96 V 0.2537 0.1559 0.5904 97 C 0.1087 0.1631 0.7282 98 S 0.0354 0.5578 0.4068 99 N 0.0223 0.7269 0.2508 100 M 0.0251 0.7992 0.1757 101 R 0.0169 0.8740 0.1091 102 A 0.0163 0.9036 0.0800 103 D 0.0125 0.9160 0.0715 104 L 0.0108 0.9108 0.0784 105 E 0.0120 0.8903 0.0978 106 A 0.0143 0.8196 0.1662 107 I 0.0235 0.6490 0.3275 108 L 0.0771 0.2663 0.6566 109 P 0.0486 0.2158 0.7356 110 E 0.0479 0.2532 0.6989 111 R 0.1359 0.2004 0.6637 112 F 0.4726 0.0824 0.4450 113 I 0.6934 0.0499 0.2567 114 F 0.7940 0.0329 0.1732 115 T 0.7482 0.0393 0.2125 116 E 0.6577 0.0510 0.2912 117 D 0.3640 0.0569 0.5792 118 R 0.1057 0.2127 0.6816 119 A 0.0651 0.1731 0.7618 120 Y 0.1242 0.2144 0.6613 121 A 0.2057 0.1356 0.6587 122 D 0.2911 0.1285 0.5804 123 Y 0.6304 0.1074 0.2622 124 I 0.7550 0.0947 0.1503 125 Y 0.6950 0.1054 0.1996 126 L 0.5661 0.1261 0.3078 127 R 0.2314 0.5027 0.2659 128 S 0.1009 0.6405 0.2586 129 D 0.0871 0.6593 0.2536 130 L 0.0760 0.6815 0.2425 131 A 0.0853 0.5317 0.3830 132 T 0.1016 0.4015 0.4968 133 L 0.1077 0.1949 0.6974 134 K 0.0553 0.2297 0.7151 135 G 0.0388 0.2195 0.7417 136 K 0.0761 0.4414 0.4825 137 K 0.0782 0.6105 0.3114 138 F 0.0378 0.7570 0.2051 139 Q 0.0414 0.7750 0.1836 140 A 0.0372 0.7769 0.1859 141 K 0.0318 0.8427 0.1255 142 R 0.0202 0.8879 0.0919 143 N 0.0180 0.8990 0.0830 144 H 0.0119 0.9217 0.0663 145 I 0.0079 0.9317 0.0604 146 N 0.0085 0.9330 0.0585 147 R 0.0081 0.9348 0.0571 148 F 0.0081 0.9281 0.0637 149 R 0.0103 0.9101 0.0797 150 N 0.0133 0.8301 0.1565 151 T 0.0232 0.6402 0.3366 152 Y 0.0713 0.1132 0.8155 153 P 0.0248 0.1156 0.8595 154 D 0.0452 0.0978 0.8570 155 Y 0.2370 0.0529 0.7101 156 E 0.4681 0.0345 0.4974 157 Y 0.5639 0.0288 0.4073 158 T 0.4725 0.0280 0.4995 159 P 0.3631 0.0324 0.6045 160 I 0.1703 0.0229 0.8068 161 T 0.0773 0.0204 0.9023 162 P 0.0077 0.7539 0.2384 163 D 0.0061 0.8126 0.1813 164 R 0.0109 0.8526 0.1365 165 I 0.0053 0.9426 0.0521 166 Q 0.0048 0.9506 0.0446 167 E 0.0048 0.9529 0.0423 168 C 0.0047 0.9578 0.0375 169 L 0.0047 0.9581 0.0372 170 D 0.0048 0.9543 0.0410 171 L 0.0048 0.9519 0.0433 172 E 0.0049 0.9508 0.0443 173 A 0.0051 0.9453 0.0496 174 E 0.0055 0.9402 0.0543 175 W 0.0070 0.9248 0.0682 176 C 0.0116 0.8859 0.1025 177 K 0.0121 0.8443 0.1436 178 V 0.0223 0.7086 0.2691 179 N 0.0356 0.4790 0.4853 180 N 0.0445 0.3032 0.6523 181 C 0.0467 0.2959 0.6574 182 D 0.0402 0.3088 0.6510 183 Q 0.0471 0.2302 0.7227 184 Q 0.0609 0.2224 0.7167 185 E 0.0398 0.4303 0.5299 186 G 0.0513 0.4906 0.4580 187 T 0.0428 0.6416 0.3156 188 G 0.0225 0.7958 0.1816 189 N 0.0159 0.8446 0.1395 190 E 0.0071 0.9155 0.0775 191 R 0.0058 0.9394 0.0548 192 R 0.0050 0.9485 0.0465 193 A 0.0050 0.9514 0.0436 194 L 0.0047 0.9552 0.0401 195 I 0.0048 0.9557 0.0395 196 Y 0.0047 0.9505 0.0448 197 A 0.0050 0.9394 0.0556 198 L 0.0056 0.9244 0.0700 199 H 0.0057 0.8519 0.1424 200 N 0.0100 0.7354 0.2546 201 F 0.0308 0.6629 0.3063 202 E 0.0119 0.6295 0.3585 203 A 0.0174 0.5781 0.4045 204 L 0.0735 0.2832 0.6433 205 G 0.1030 0.0833 0.8137 206 L 0.2914 0.0290 0.6795 207 T 0.5517 0.0407 0.4076 208 G 0.7874 0.0159 0.1966 209 G 0.9026 0.0048 0.0925 210 I 0.9261 0.0034 0.0705 211 L 0.9262 0.0037 0.0702 212 H 0.9176 0.0034 0.0789 213 V 0.8319 0.0144 0.1537 214 N 0.0782 0.0257 0.8961 215 G 0.0384 0.0404 0.9212 216 K 0.7218 0.0077 0.2705 217 I 0.9192 0.0030 0.0777 218 V 0.8730 0.0251 0.1019 219 A 0.9207 0.0052 0.0741 220 F 0.9174 0.0044 0.0782 221 T 0.8993 0.0046 0.0961 222 F 0.8184 0.0211 0.1606 223 G 0.6492 0.0470 0.3038 224 M 0.6158 0.0664 0.3178 225 P 0.6343 0.0466 0.3191 226 I 0.5452 0.0333 0.4215 227 N 0.1937 0.0281 0.7781 228 H 0.0174 0.1051 0.8774 229 E 0.0460 0.0695 0.8845 230 T 0.6545 0.0168 0.3287 231 F 0.8963 0.0083 0.0953 232 G 0.9300 0.0040 0.0660 233 V 0.9275 0.0039 0.0686 234 H 0.9166 0.0052 0.0783 235 V 0.8532 0.0196 0.1273 236 E 0.7047 0.0397 0.2555 237 K 0.5142 0.0747 0.4112 238 A 0.2535 0.0888 0.6577 239 D 0.0842 0.1086 0.8072 240 T 0.0169 0.3181 0.6650 241 S 0.0355 0.3311 0.6334 242 I 0.0938 0.6044 0.3018 243 D 0.0707 0.6909 0.2384 244 G 0.0748 0.7227 0.2025 245 A 0.0308 0.8850 0.0842 246 Y 0.0258 0.9122 0.0620 247 A 0.0121 0.9240 0.0639 248 M 0.0104 0.9347 0.0550 249 I 0.0134 0.9193 0.0674 250 N 0.0099 0.9160 0.0741 251 Y 0.0059 0.9367 0.0574 252 E 0.0071 0.9333 0.0596 253 F 0.0055 0.9361 0.0584 254 A 0.0068 0.9228 0.0704 255 N 0.0095 0.9042 0.0863 256 R 0.0133 0.8141 0.1726 257 I 0.0311 0.6345 0.3343 258 P 0.0442 0.4344 0.5214 259 E 0.0482 0.3004 0.6514 260 Q 0.0950 0.1514 0.7536 261 Y 0.3630 0.0493 0.5877 262 I 0.7111 0.0344 0.2545 263 Y 0.8014 0.0384 0.1602 264 I 0.6935 0.0526 0.2540 265 N 0.4381 0.0692 0.4927 266 R 0.0501 0.4444 0.5055 267 E 0.0326 0.5493 0.4180 268 E 0.0300 0.6343 0.3358 269 D 0.0382 0.5062 0.4556 270 L 0.0525 0.3199 0.6276 271 G 0.0512 0.1238 0.8250 272 I 0.0445 0.3688 0.5867 273 E 0.0164 0.5753 0.4082 274 G 0.0227 0.5253 0.4519 275 L 0.0498 0.7186 0.2315 276 R 0.0224 0.8238 0.1538 277 K 0.0299 0.8062 0.1639 278 A 0.0605 0.7610 0.1785 279 K 0.0798 0.6834 0.2368 280 L 0.1091 0.5838 0.3071 281 S 0.1387 0.4343 0.4270 282 Y 0.1710 0.2403 0.5887 283 Q 0.1932 0.0654 0.7414 284 P 0.1618 0.1795 0.6587 285 V 0.1221 0.4661 0.4118 286 T 0.2841 0.3990 0.3169 287 I 0.4028 0.3520 0.2452 288 L 0.4918 0.2316 0.2766 289 E 0.5518 0.2139 0.2343 290 K 0.5990 0.1649 0.2362 291 Y 0.6795 0.0936 0.2269 292 M 0.7445 0.0676 0.1880 293 A 0.7328 0.0581 0.2091 294 C 0.6578 0.0640 0.2782 295 L 0.3603 0.0635 0.5761 296 K 0.0787 0.1289 0.7924 297 D 0.0600 0.0754 0.8646 298 H 0.1035 0.0498 0.8467 299 P 0.1174 0.1336 0.7490 300 M 0.1622 0.2997 0.5381 301 D 0.2187 0.3123 0.4690 302 M 0.3489 0.2123 0.4388 303 V 0.4412 0.1030 0.4558 304 R 0.2877 0.0801 0.6323 305 W 0.0521 0.0351 0.9128