# This file is the result of combining several RDB files, specifically # T0642.t04.dssp-ebghstl.rdb (weight 1.53986) # T0642.t04.stride-ebghtl.rdb (weight 1.24869) # T0642.t04.str2.rdb (weight 1.54758) # T0642.t04.alpha.rdb (weight 0.659012) # T0642.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0642.t2k.stride-ebghtl.rdb (weight 1.24869) # T0642.t2k.str2.rdb (weight 1.54758) # T0642.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 T0642.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0642 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0642.t04-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 1 # # ============================================ # Comments from T0642.t04.stride-ebghtl.rdb # ============================================ # TARGET T0642 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0642.t04-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 1 # # ============================================ # Comments from T0642.t04.str2.rdb # ============================================ # TARGET T0642 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.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 T0642.t04-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 1 # # ============================================ # Comments from T0642.t04.alpha.rdb # ============================================ # TARGET T0642 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0642.t04-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 1 # # ============================================ # Comments from T0642.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0642 # 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 T0642.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 1 # # ============================================ # Comments from T0642.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0642 # 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 T0642.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 1 # # ============================================ # Comments from T0642.t2k.str2.rdb # ============================================ # TARGET T0642 # 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 T0642.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 1 # # ============================================ # Comments from T0642.t2k.alpha.rdb # ============================================ # TARGET T0642 # 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 T0642.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0545 0.0819 0.8637 2 D 0.1021 0.1657 0.7322 3 E 0.0819 0.3440 0.5742 4 A 0.0896 0.3999 0.5104 5 R 0.1287 0.3643 0.5069 6 C 0.1495 0.2521 0.5984 7 A 0.1258 0.1833 0.6909 8 S 0.1050 0.1111 0.7840 9 P 0.0598 0.2682 0.6720 10 E 0.0662 0.2712 0.6627 11 R 0.0860 0.2464 0.6675 12 S 0.1157 0.1811 0.7032 13 T 0.1693 0.1798 0.6509 14 E 0.2672 0.1794 0.5534 15 R 0.3982 0.1435 0.4584 16 R 0.5839 0.0949 0.3212 17 I 0.7417 0.0574 0.2008 18 F 0.8063 0.0440 0.1497 19 I 0.8030 0.0419 0.1552 20 C 0.6267 0.0622 0.3110 21 N 0.3626 0.1072 0.5302 22 E 0.2437 0.1987 0.5575 23 W 0.2671 0.1983 0.5346 24 S 0.2500 0.2000 0.5499 25 Y 0.1889 0.2653 0.5459 26 E 0.1399 0.3104 0.5497 27 S 0.1176 0.3249 0.5574 28 T 0.0913 0.3510 0.5577 29 E 0.0760 0.4312 0.4928 30 R 0.0577 0.5103 0.4320 31 D 0.0541 0.5608 0.3851 32 A 0.0510 0.6798 0.2692 33 Y 0.0571 0.7107 0.2322 34 W 0.0625 0.7250 0.2125 35 E 0.0578 0.7591 0.1831 36 R 0.0593 0.7490 0.1917 37 E 0.0667 0.7236 0.2097 38 L 0.0738 0.6676 0.2587 39 E 0.0834 0.5707 0.3458 40 A 0.0645 0.5312 0.4043 41 S 0.0697 0.4028 0.5275 42 E 0.0534 0.4180 0.5286 43 D 0.0709 0.3688 0.5603 44 T 0.0774 0.4642 0.4584 45 H 0.1032 0.4748 0.4220 46 E 0.1366 0.4975 0.3659 47 L 0.1498 0.4975 0.3528 48 A 0.1532 0.4193 0.4275 49 S 0.1564 0.3496 0.4940 50 T 0.1294 0.3492 0.5214 51 S 0.1232 0.4050 0.4717 52 E 0.1453 0.4450 0.4097 53 Q 0.2017 0.3943 0.4040 54 I 0.2359 0.3193 0.4448 55 N 0.2129 0.2530 0.5341 56 T 0.1564 0.3060 0.5375 57 H 0.1441 0.3124 0.5435 58 E 0.1356 0.3317 0.5327 59 N 0.1611 0.2448 0.5941 60 I 0.1942 0.2114 0.5944 61 N 0.1934 0.1682 0.6384 62 T 0.1891 0.2354 0.5755 63 H 0.2118 0.2093 0.5790 64 C 0.2062 0.1784 0.6154 65 A 0.1620 0.1319 0.7061 66 S 0.1164 0.1043 0.7793 67 P 0.0999 0.1068 0.7933 68 P 0.1487 0.1586 0.6926 69 L 0.1722 0.2295 0.5983 70 E 0.1915 0.2247 0.5838 71 A 0.1422 0.2448 0.6131 72 S 0.1097 0.2034 0.6870 73 E 0.0796 0.2064 0.7140 74 G 0.0701 0.1523 0.7777 75 E 0.1291 0.1421 0.7288 76 T 0.2029 0.1663 0.6307 77 R 0.1644 0.2622 0.5734 78 E 0.1419 0.2709 0.5872 79 S 0.1348 0.2783 0.5869 80 T 0.1148 0.3067 0.5785 81 E 0.0902 0.3332 0.5766 82 D 0.0941 0.3132 0.5927 83 A 0.0459 0.4926 0.4615 84 N 0.0467 0.4377 0.5156 85 D 0.0711 0.4568 0.4721 86 L 0.0775 0.5155 0.4070 87 E 0.0918 0.4913 0.4169 88 T 0.1065 0.4653 0.4282 89 A 0.0933 0.4357 0.4709 90 S 0.0964 0.3520 0.5516 91 S 0.0870 0.3561 0.5568 92 E 0.0750 0.4294 0.4956 93 S 0.0817 0.4218 0.4965 94 S 0.0873 0.3908 0.5219 95 M 0.0973 0.3836 0.5192 96 E 0.0868 0.3452 0.5681 97 N 0.0969 0.2446 0.6585 98 T 0.0710 0.2696 0.6594 99 D 0.0694 0.3044 0.6262 100 E 0.0624 0.5282 0.4094 101 T 0.0716 0.5826 0.3458 102 E 0.0900 0.6357 0.2743 103 R 0.1319 0.6279 0.2402 104 M 0.1586 0.5906 0.2508 105 I 0.1852 0.5206 0.2942 106 N 0.1569 0.4571 0.3860 107 E 0.1050 0.4908 0.4042 108 T 0.1026 0.4351 0.4624 109 H 0.1048 0.3764 0.5188 110 E 0.0923 0.3852 0.5224 111 E 0.1029 0.3597 0.5374 112 S 0.1258 0.2991 0.5751 113 T 0.1457 0.3263 0.5280 114 S 0.2093 0.3094 0.4813 115 C 0.2790 0.2749 0.4461 116 I 0.3306 0.2378 0.4316 117 E 0.3172 0.2253 0.4575 118 N 0.3162 0.1612 0.5226 119 T 0.5590 0.0819 0.3591 120 I 0.7873 0.0410 0.1717 121 F 0.8599 0.0266 0.1136 122 I 0.8522 0.0297 0.1181 123 C 0.7976 0.0302 0.1722 124 C 0.5705 0.0580 0.3715 125 E 0.2954 0.1082 0.5964 126 N 0.1982 0.1032 0.6986 127 T 0.1903 0.1252 0.6845 128 E 0.2046 0.1515 0.6439 129 R 0.2642 0.1596 0.5762 130 S 0.2868 0.1550 0.5582 131 T 0.3331 0.1612 0.5057 132 H 0.4149 0.1435 0.4416 133 I 0.4090 0.1705 0.4205 134 S 0.3935 0.1843 0.4222 135 T 0.2579 0.2339 0.5082 136 A 0.1782 0.2504 0.5714 137 R 0.1191 0.2167 0.6642 138 G 0.1105 0.1654 0.7241 139 E 0.2195 0.1565 0.6240 140 T 0.3592 0.1702 0.4706 141 I 0.2325 0.4128 0.3547 142 S 0.1939 0.4761 0.3301 143 D 0.1919 0.5327 0.2754 144 I 0.2760 0.4878 0.2362 145 F 0.3644 0.3981 0.2375 146 F 0.3579 0.3528 0.2894 147 E 0.2824 0.3439 0.3737 148 R 0.2084 0.3341 0.4575 149 E 0.1447 0.3088 0.5465 150 N 0.1167 0.2243 0.6591 151 T 0.1161 0.2142 0.6697 152 A 0.0872 0.2590 0.6539 153 N 0.0832 0.2319 0.6849 154 D 0.0819 0.2396 0.6785 155 H 0.1155 0.2573 0.6271 156 A 0.1710 0.2878 0.5412 157 S 0.2351 0.2737 0.4912 158 V 0.2451 0.3385 0.4164 159 E 0.2541 0.3206 0.4253 160 R 0.2662 0.2375 0.4963 161 Y 0.2267 0.1351 0.6382 162 S 0.1403 0.0585 0.8011 163 P 0.0673 0.3375 0.5952 164 E 0.1331 0.3543 0.5125 165 C 0.4346 0.2657 0.2997 166 I 0.6224 0.1709 0.2067 167 F 0.7335 0.1037 0.1628 168 I 0.6608 0.1320 0.2071 169 C 0.4134 0.1816 0.4050 170 S 0.1778 0.2019 0.6203 171 H 0.1071 0.1559 0.7370 172 A 0.1113 0.1409 0.7477 173 P 0.0796 0.4086 0.5118 174 E 0.1476 0.5250 0.3274 175 W 0.2835 0.5065 0.2100 176 I 0.4193 0.4207 0.1599 177 L 0.5487 0.2991 0.1522 178 L 0.5114 0.2851 0.2036 179 C 0.4377 0.2696 0.2927 180 H 0.3070 0.2860 0.4070 181 E 0.3072 0.2292 0.4636 182 C 0.3957 0.1399 0.4643 183 K 0.5155 0.0932 0.3913 184 I 0.6046 0.0817 0.3137 185 T 0.5296 0.1084 0.3620 186 A 0.4239 0.1775 0.3986 187 T 0.3277 0.2006 0.4717 188 T 0.2391 0.3158 0.4451 189 H 0.1616 0.4352 0.4032 190 E 0.1502 0.5220 0.3277 191 M 0.1163 0.5919 0.2918 192 E 0.1118 0.5945 0.2937 193 E 0.1217 0.5767 0.3017 194 T 0.1170 0.5291 0.3539 195 I 0.1234 0.4413 0.4352 196 N 0.0712 0.2816 0.6472 197 G 0.0714 0.1620 0.7666 198 I 0.1432 0.1004 0.7564 199 N 0.1128 0.0641 0.8231 200 P 0.0449 0.6266 0.3286 201 A 0.0678 0.6720 0.2603 202 C 0.1746 0.6487 0.1767 203 I 0.3414 0.5045 0.1541 204 F 0.4384 0.3999 0.1617 205 I 0.3930 0.4086 0.1984 206 C 0.2237 0.4135 0.3628 207 G 0.1381 0.3458 0.5161 208 R 0.1588 0.3988 0.4424 209 V 0.1795 0.4744 0.3461 210 E 0.1604 0.4806 0.3590 211 H 0.1374 0.4897 0.3730 212 A 0.0744 0.6512 0.2744 213 H 0.0801 0.6421 0.2778 214 A 0.0816 0.6608 0.2576 215 L 0.0779 0.6741 0.2480 216 A 0.0617 0.6916 0.2467 217 S 0.0563 0.6941 0.2495 218 T 0.0635 0.7439 0.1926 219 W 0.0870 0.7772 0.1358 220 C 0.1103 0.7682 0.1215 221 F 0.0884 0.7956 0.1160 222 I 0.0572 0.8347 0.1081 223 N 0.0550 0.8233 0.1217 224 A 0.0569 0.8043 0.1388 225 L 0.0908 0.7431 0.1662 226 I 0.1104 0.6950 0.1946 227 S 0.1107 0.6352 0.2541 228 T 0.1054 0.6157 0.2789 229 S 0.1605 0.5416 0.2979 230 I 0.1958 0.5878 0.2164 231 T 0.2118 0.5979 0.1903 232 A 0.2312 0.5927 0.1761 233 L 0.2282 0.5514 0.2205 234 Y 0.2216 0.4764 0.3020 235 A 0.1084 0.5536 0.3380 236 N 0.0699 0.4695 0.4606 237 D 0.0800 0.4109 0.5091 238 F 0.1174 0.4234 0.4592 239 R 0.1203 0.4264 0.4533 240 A 0.0819 0.4811 0.4370 241 N 0.0969 0.3731 0.5300 242 C 0.1325 0.3540 0.5135 243 E 0.1561 0.3931 0.4508 244 W 0.1638 0.4155 0.4207 245 E 0.1734 0.4010 0.4256 246 R 0.1621 0.4723 0.3656 247 E 0.1770 0.4671 0.3560 248 E 0.2755 0.4139 0.3105 249 L 0.5096 0.2587 0.2317 250 I 0.6011 0.2127 0.1862 251 M 0.6361 0.1811 0.1829 252 I 0.5312 0.1862 0.2826 253 N 0.3739 0.1590 0.4671 254 A 0.1812 0.2436 0.5752 255 T 0.1315 0.2537 0.6148 256 E 0.1033 0.2425 0.6542 257 D 0.1124 0.1705 0.7171 258 I 0.1508 0.1108 0.7384 259 N 0.0997 0.0560 0.8443 260 P 0.0352 0.5697 0.3951 261 R 0.0387 0.6532 0.3081 262 E 0.0806 0.7039 0.2155 263 L 0.2412 0.5608 0.1980 264 I 0.3659 0.4696 0.1645 265 M 0.4381 0.4086 0.1533 266 I 0.3410 0.4530 0.2059 267 N 0.2997 0.4074 0.2929 268 A 0.1225 0.6687 0.2088 269 R 0.1364 0.6484 0.2152 270 Y 0.1514 0.6405 0.2081 271 M 0.1581 0.6160 0.2258 272 A 0.1454 0.5875 0.2671 273 T 0.1284 0.5387 0.3329 274 C 0.1190 0.4285 0.4525 275 H 0.0923 0.3347 0.5730 276 E 0.0588 0.3278 0.6134 277 S 0.0550 0.2993 0.6456 278 S 0.0696 0.2365 0.6939 279 P 0.0630 0.4365 0.5004 280 A 0.1009 0.5363 0.3628 281 I 0.1546 0.5475 0.2979 282 N 0.2339 0.4916 0.2746 283 W 0.2809 0.4665 0.2526 284 I 0.3102 0.4074 0.2823 285 N 0.2857 0.3430 0.3713 286 A 0.1447 0.3619 0.4934 287 G 0.1386 0.2428 0.6186 288 A 0.2314 0.2291 0.5395 289 I 0.3112 0.1890 0.4997 290 N 0.2061 0.1752 0.6187 291 S 0.1437 0.1786 0.6777 292 T 0.1086 0.2204 0.6710 293 N 0.0963 0.2381 0.6656 294 E 0.1106 0.3706 0.5188 295 T 0.1281 0.4463 0.4256 296 H 0.1125 0.5506 0.3369 297 E 0.1177 0.5925 0.2897 298 R 0.1069 0.5992 0.2940 299 L 0.0978 0.5845 0.3177 300 A 0.0664 0.5783 0.3553 301 N 0.0524 0.5061 0.4415 302 D 0.0564 0.4506 0.4930 303 S 0.0820 0.5120 0.4059 304 I 0.0956 0.6683 0.2361 305 N 0.0878 0.7237 0.1885 306 F 0.0752 0.7851 0.1398 307 I 0.0700 0.8225 0.1075 308 N 0.0826 0.7961 0.1213 309 A 0.0913 0.7835 0.1252 310 L 0.1125 0.7373 0.1501 311 I 0.1368 0.6281 0.2351 312 N 0.1384 0.4470 0.4147 313 T 0.1155 0.3605 0.5241 314 E 0.1239 0.3813 0.4948 315 R 0.1416 0.3779 0.4805 316 E 0.1323 0.3785 0.4893 317 S 0.1749 0.3221 0.5030 318 T 0.2213 0.2541 0.5246 319 I 0.2144 0.2016 0.5840 320 N 0.1538 0.1540 0.6922 321 G 0.1086 0.1565 0.7349 322 E 0.1140 0.2219 0.6642 323 N 0.1454 0.2185 0.6362 324 D 0.1528 0.1854 0.6618 325 I 0.1537 0.2189 0.6275 326 N 0.1257 0.1942 0.6801 327 G 0.1074 0.2576 0.6350 328 H 0.1743 0.3304 0.4953 329 A 0.2785 0.3794 0.3421 330 V 0.2910 0.3948 0.3141 331 E 0.2350 0.4558 0.3092 332 A 0.1269 0.6005 0.2727 333 N 0.1164 0.5953 0.2883 334 I 0.1030 0.7034 0.1936 335 C 0.1068 0.7199 0.1733 336 E 0.0829 0.7763 0.1408 337 F 0.0642 0.8335 0.1022 338 A 0.0611 0.8407 0.0982 339 L 0.0649 0.8315 0.1036 340 L 0.0652 0.8051 0.1297 341 M 0.0724 0.7556 0.1720 342 E 0.0716 0.7184 0.2101 343 R 0.0661 0.6900 0.2439 344 R 0.0741 0.6398 0.2861 345 Y 0.0972 0.5874 0.3153 346 C 0.1172 0.5363 0.3465 347 H 0.1406 0.4928 0.3666 348 R 0.1841 0.4676 0.3483 349 I 0.2086 0.4580 0.3333 350 S 0.2277 0.4283 0.3440 351 T 0.2010 0.4476 0.3515 352 M 0.1892 0.4364 0.3744 353 A 0.1728 0.3697 0.4575 354 S 0.1523 0.2889 0.5588 355 A 0.0808 0.2911 0.6281 356 N 0.0669 0.2207 0.7124 357 D 0.0612 0.2007 0.7381 358 H 0.0693 0.1691 0.7616 359 A 0.0760 0.1238 0.8003 360 P 0.0678 0.1263 0.8059 361 P 0.0712 0.2538 0.6750 362 Y 0.0633 0.3973 0.5394 363 N 0.0566 0.5010 0.4423 364 E 0.0563 0.6458 0.2979 365 W 0.0576 0.6984 0.2439 366 Y 0.0740 0.6701 0.2558 367 E 0.0706 0.6625 0.2669 368 A 0.0592 0.6506 0.2902 369 R 0.0714 0.5807 0.3479 370 T 0.0793 0.5519 0.3688 371 A 0.0559 0.6509 0.2932 372 K 0.0629 0.6629 0.2742 373 E 0.0921 0.6367 0.2711 374 I 0.1235 0.5624 0.3141 375 T 0.1392 0.5120 0.3489 376 E 0.1171 0.5790 0.3039 377 A 0.1046 0.5547 0.3407 378 S 0.1136 0.4757 0.4106 379 Y 0.1177 0.4088 0.4735 380 A 0.0875 0.3972 0.5153 381 N 0.0769 0.3048 0.6183 382 D 0.0786 0.3134 0.6080 383 S 0.1680 0.3043 0.5278 384 M 0.3198 0.2395 0.4407 385 I 0.3582 0.1576 0.4842 386 L 0.1864 0.1198 0.6937 387 E 0.0443 0.0431 0.9126