# This file is the result of combining several RDB files, specifically # T0398.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0398.t2k.stride-ebghtl.rdb (weight 1.24869) # T0398.t2k.str.rdb (weight 1.53983) # 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 T0398.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0398 # 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 T0398.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 789 # # ============================================ # Comments from T0398.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0398 # 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 T0398.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 789 # # ============================================ # Comments from T0398.t2k.str.rdb # ============================================ # TARGET T0398 # 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 T0398.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 789 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0777 0.0417 0.8806 2 L 0.1122 0.0792 0.8086 3 T 0.2956 0.0682 0.6361 4 G 0.5078 0.0507 0.4415 5 K 0.7755 0.0222 0.2023 6 H 0.8883 0.0150 0.0967 7 V 0.8795 0.0141 0.1064 8 V 0.8135 0.0172 0.1693 9 I 0.4470 0.0315 0.5215 10 I 0.0467 0.5746 0.3787 11 G 0.0102 0.7864 0.2034 12 G 0.0051 0.9281 0.0668 13 D 0.0040 0.9693 0.0267 14 A 0.0051 0.9689 0.0260 15 R 0.0054 0.9676 0.0269 16 Q 0.0051 0.9648 0.0301 17 L 0.0061 0.9491 0.0447 18 E 0.0072 0.8728 0.1201 19 I 0.0099 0.6351 0.3550 20 I 0.0377 0.2167 0.7456 21 R 0.0872 0.1033 0.8095 22 K 0.3329 0.1022 0.5650 23 L 0.6796 0.0733 0.2471 24 S 0.8483 0.0511 0.1006 25 T 0.8459 0.0507 0.1034 26 F 0.6373 0.0866 0.2761 27 D 0.2022 0.1798 0.6180 28 A 0.1026 0.1994 0.6980 29 K 0.2631 0.2739 0.4630 30 I 0.4765 0.2616 0.2619 31 S 0.5378 0.2786 0.1836 32 L 0.5893 0.2335 0.1772 33 V 0.5377 0.1752 0.2871 34 G 0.4771 0.0978 0.4251 35 F 0.3274 0.0593 0.6133 36 D 0.1420 0.0689 0.7891 37 Q 0.0305 0.5228 0.4467 38 L 0.0157 0.7537 0.2306 39 D 0.0234 0.8418 0.1348 40 D 0.0589 0.7990 0.1421 41 G 0.0927 0.7731 0.1343 42 F 0.0924 0.7322 0.1754 43 I 0.0645 0.5599 0.3756 44 G 0.0748 0.1912 0.7341 45 V 0.2279 0.1636 0.6085 46 T 0.4704 0.1496 0.3799 47 K 0.4520 0.1597 0.3884 48 M 0.2821 0.1389 0.5789 49 R 0.1339 0.1936 0.6725 50 I 0.0597 0.3010 0.6394 51 D 0.0244 0.6631 0.3124 52 E 0.0193 0.7730 0.2077 53 V 0.0224 0.8034 0.1741 54 D 0.0278 0.7853 0.1869 55 W 0.0407 0.7590 0.2003 56 N 0.0563 0.6121 0.3316 57 T 0.0759 0.3912 0.5329 58 V 0.1644 0.1616 0.6740 59 D 0.2618 0.0825 0.6557 60 A 0.6741 0.0430 0.2828 61 I 0.8257 0.0194 0.1549 62 L 0.8699 0.0115 0.1186 63 L 0.7935 0.0089 0.1976 64 P 0.4945 0.0096 0.4959 65 I 0.2779 0.0135 0.7086 66 S 0.1663 0.0162 0.8175 67 G 0.1116 0.0253 0.8631 68 T 0.1317 0.0516 0.8167 69 N 0.0572 0.2385 0.7043 70 E 0.0245 0.3506 0.6250 71 A 0.0372 0.4217 0.5412 72 G 0.0960 0.4046 0.4994 73 K 0.1619 0.4201 0.4180 74 V 0.2440 0.4580 0.2979 75 D 0.2982 0.4104 0.2914 76 T 0.2769 0.3982 0.3248 77 I 0.1846 0.4379 0.3774 78 F 0.1162 0.4280 0.4558 79 S 0.0923 0.4369 0.4708 80 N 0.1157 0.3885 0.4958 81 E 0.1999 0.4203 0.3798 82 S 0.2306 0.4928 0.2765 83 I 0.1974 0.5577 0.2449 84 V 0.1609 0.6201 0.2190 85 L 0.1275 0.6295 0.2430 86 T 0.0870 0.6807 0.2323 87 E 0.0365 0.8018 0.1617 88 E 0.0266 0.7523 0.2211 89 M 0.0305 0.6850 0.2846 90 I 0.0254 0.5502 0.4244 91 E 0.0244 0.3676 0.6080 92 K 0.0377 0.2764 0.6859 93 T 0.0663 0.2529 0.6809 94 P 0.0985 0.2718 0.6297 95 N 0.1643 0.2729 0.5629 96 H 0.3400 0.1970 0.4630 97 C 0.5272 0.1574 0.3155 98 V 0.6463 0.1341 0.2196 99 V 0.7131 0.1266 0.1604 100 Y 0.7465 0.1212 0.1323 101 S 0.6892 0.1365 0.1743 102 G 0.5562 0.1409 0.3029 103 I 0.4416 0.1313 0.4271 104 S 0.3435 0.1245 0.5321 105 N 0.2255 0.2742 0.5002 106 T 0.1256 0.4988 0.3757 107 Y 0.0967 0.5899 0.3134 108 L 0.0728 0.6192 0.3080 109 N 0.0561 0.6372 0.3067 110 Q 0.0536 0.6201 0.3263 111 C 0.0697 0.6442 0.2861 112 M 0.0698 0.7102 0.2200 113 K 0.0447 0.7740 0.1813 114 K 0.0356 0.7808 0.1836 115 T 0.0220 0.8333 0.1447 116 N 0.0340 0.8175 0.1485 117 R 0.0512 0.8031 0.1457 118 T 0.0562 0.7506 0.1932 119 L 0.0463 0.7797 0.1740 120 V 0.0354 0.8102 0.1544 121 K 0.0228 0.8016 0.1756 122 L 0.0219 0.7855 0.1925 123 M 0.0246 0.6938 0.2816 124 E 0.0228 0.6741 0.3031 125 R 0.0158 0.7472 0.2371 126 D 0.0147 0.7615 0.2237 127 D 0.0126 0.8014 0.1860 128 I 0.0152 0.8688 0.1160 129 A 0.0112 0.8840 0.1048 130 I 0.0109 0.9014 0.0877 131 Y 0.0101 0.8917 0.0982 132 N 0.0119 0.8661 0.1220 133 S 0.0160 0.8356 0.1484 134 I 0.0213 0.8452 0.1335 135 P 0.0234 0.8525 0.1241 136 T 0.0197 0.8590 0.1213 137 A 0.0180 0.8733 0.1086 138 E 0.0200 0.8735 0.1066 139 G 0.0267 0.8458 0.1275 140 T 0.0329 0.8275 0.1396 141 I 0.0402 0.7813 0.1785 142 M 0.0355 0.7299 0.2346 143 M 0.0360 0.6772 0.2868 144 A 0.0581 0.5369 0.4050 145 I 0.0744 0.4110 0.5145 146 Q 0.0752 0.2648 0.6599 147 H 0.1050 0.1911 0.7038 148 T 0.1663 0.1133 0.7204 149 D 0.2575 0.0747 0.6679 150 F 0.5565 0.0443 0.3992 151 T 0.6967 0.0265 0.2768 152 I 0.5585 0.0331 0.4085 153 H 0.1403 0.0542 0.8054 154 G 0.0432 0.0329 0.9240 155 A 0.2870 0.0123 0.7008 156 N 0.8422 0.0027 0.1551 157 V 0.9711 0.0024 0.0265 158 A 0.9796 0.0024 0.0180 159 V 0.9763 0.0024 0.0213 160 L 0.9077 0.0028 0.0895 161 G 0.5156 0.0076 0.4768 162 L 0.1190 0.0472 0.8338 163 G 0.0236 0.1641 0.8123 164 R 0.0038 0.9413 0.0549 165 V 0.0037 0.9590 0.0372 166 G 0.0037 0.9738 0.0225 167 M 0.0037 0.9762 0.0200 168 S 0.0037 0.9759 0.0204 169 V 0.0037 0.9762 0.0200 170 A 0.0037 0.9762 0.0200 171 R 0.0037 0.9749 0.0214 172 K 0.0037 0.9715 0.0248 173 F 0.0037 0.9647 0.0316 174 A 0.0038 0.9464 0.0497 175 A 0.0039 0.8577 0.1384 176 L 0.0054 0.3347 0.6600 177 G 0.0098 0.0065 0.9837 178 A 0.0618 0.0048 0.9334 179 K 0.7493 0.0032 0.2475 180 V 0.9622 0.0024 0.0354 181 K 0.9770 0.0024 0.0206 182 V 0.9740 0.0024 0.0236 183 G 0.9080 0.0026 0.0894 184 A 0.4984 0.0048 0.4968 185 R 0.0560 0.0133 0.9307 186 E 0.0329 0.0226 0.9444 187 S 0.0069 0.6560 0.3371 188 D 0.0067 0.7452 0.2481 189 L 0.0063 0.8320 0.1617 190 L 0.0056 0.8840 0.1104 191 A 0.0090 0.8833 0.1077 192 R 0.0096 0.9102 0.0802 193 I 0.0095 0.9123 0.0782 194 A 0.0066 0.9234 0.0701 195 E 0.0060 0.8711 0.1229 196 M 0.0059 0.6017 0.3924 197 G 0.0139 0.1394 0.8467 198 M 0.0492 0.0825 0.8683 199 E 0.1453 0.1367 0.7180 200 P 0.2972 0.2073 0.4955 201 F 0.3287 0.1890 0.4823 202 H 0.3236 0.1820 0.4944 203 I 0.1214 0.4183 0.4603 204 S 0.0658 0.4782 0.4560 205 K 0.0549 0.5213 0.4238 206 A 0.0748 0.4672 0.4580 207 A 0.1005 0.4833 0.4163 208 Q 0.1408 0.4062 0.4530 209 E 0.3035 0.3081 0.3884 210 L 0.5138 0.1868 0.2994 211 R 0.6480 0.1712 0.1808 212 D 0.7191 0.1762 0.1047 213 V 0.7544 0.1209 0.1247 214 D 0.7212 0.0999 0.1789 215 V 0.5995 0.0522 0.3483 216 C 0.4064 0.0407 0.5529 217 I 0.2281 0.0486 0.7232 218 N 0.1029 0.0513 0.8458 219 T 0.0643 0.0696 0.8661 220 I 0.0466 0.0762 0.8773 221 P 0.0545 0.0801 0.8654 222 A 0.0504 0.2399 0.7097 223 L 0.0819 0.2822 0.6360 224 V 0.2648 0.1850 0.5502 225 V 0.3507 0.0560 0.5933 226 T 0.1249 0.0798 0.7953 227 A 0.0039 0.9532 0.0430 228 N 0.0038 0.9565 0.0398 229 V 0.0037 0.9604 0.0359 230 L 0.0041 0.9534 0.0425 231 A 0.0073 0.8531 0.1396 232 E 0.0097 0.6246 0.3657 233 M 0.0459 0.2440 0.7100 234 P 0.0573 0.0412 0.9015 235 S 0.0316 0.0549 0.9135 236 H 0.0632 0.0314 0.9055 237 T 0.6593 0.0053 0.3355 238 F 0.9742 0.0024 0.0233 239 V 0.9810 0.0024 0.0166 240 I 0.9719 0.0025 0.0256 241 D 0.9190 0.0039 0.0771 242 L 0.6229 0.0169 0.3602 243 A 0.2995 0.0389 0.6616 244 S 0.1306 0.0607 0.8087 245 K 0.0590 0.0575 0.8835 246 P 0.0582 0.0966 0.8453 247 G 0.0808 0.1455 0.7737 248 G 0.1557 0.1826 0.6617 249 T 0.1384 0.1871 0.6746 250 D 0.0358 0.5164 0.4478 251 F 0.0063 0.9125 0.0812 252 R 0.0067 0.9364 0.0569 253 Y 0.0063 0.9459 0.0478 254 A 0.0068 0.9427 0.0505 255 E 0.0078 0.9070 0.0852 256 K 0.0079 0.8361 0.1561 257 R 0.0081 0.5319 0.4600 258 G 0.0185 0.0794 0.9021 259 I 0.0897 0.0572 0.8531 260 K 0.3784 0.0406 0.5809 261 A 0.6801 0.0299 0.2900 262 L 0.7628 0.0248 0.2124 263 L 0.6906 0.0284 0.2810 264 V 0.4398 0.0381 0.5221 265 P 0.1868 0.0590 0.7543 266 G 0.1041 0.0473 0.8486 267 L 0.1808 0.0438 0.7754 268 P 0.1863 0.0455 0.7682 269 G 0.2923 0.1376 0.5701 270 I 0.3444 0.1461 0.5095 271 V 0.2971 0.1076 0.5953 272 A 0.1784 0.0684 0.7532 273 P 0.0531 0.1078 0.8391 274 K 0.0272 0.2174 0.7554 275 T 0.0372 0.3050 0.6578 276 A 0.0161 0.6255 0.3584 277 G 0.0088 0.7921 0.1991 278 R 0.0085 0.8980 0.0935 279 I 0.0081 0.9199 0.0720 280 L 0.0094 0.9154 0.0751 281 A 0.0106 0.8671 0.1223 282 D 0.0117 0.7714 0.2169 283 V 0.0254 0.7628 0.2119 284 L 0.0481 0.6941 0.2577 285 V 0.0312 0.7669 0.2019 286 K 0.0286 0.7975 0.1739 287 L 0.0364 0.8090 0.1546 288 L 0.0736 0.6705 0.2559 289 A 0.0685 0.4620 0.4695 290 E 0.0671 0.1322 0.8008 291 P 0.0376 0.0314 0.9311 292 S 0.0104 0.0048 0.9848