# This file is the result of combining several RDB files, specifically # T0550.t04.dssp-ebghstl.rdb (weight 1.53986) # T0550.t04.stride-ebghtl.rdb (weight 1.24869) # T0550.t04.str2.rdb (weight 1.54758) # T0550.t04.alpha.rdb (weight 0.659012) # T0550.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0550.t2k.stride-ebghtl.rdb (weight 1.24869) # T0550.t2k.str2.rdb (weight 1.54758) # T0550.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 T0550.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0550 # 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 T0550.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 604 # # ============================================ # Comments from T0550.t04.stride-ebghtl.rdb # ============================================ # TARGET T0550 # 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 T0550.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 604 # # ============================================ # Comments from T0550.t04.str2.rdb # ============================================ # TARGET T0550 # 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 T0550.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 604 # # ============================================ # Comments from T0550.t04.alpha.rdb # ============================================ # TARGET T0550 # 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 T0550.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 604 # # ============================================ # Comments from T0550.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0550 # 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 T0550.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 41 # # ============================================ # Comments from T0550.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0550 # 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 T0550.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 41 # # ============================================ # Comments from T0550.t2k.str2.rdb # ============================================ # TARGET T0550 # 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 T0550.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 41 # # ============================================ # Comments from T0550.t2k.alpha.rdb # ============================================ # TARGET T0550 # 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 T0550.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 41 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0162 0.3181 0.6657 2 K 0.0186 0.7045 0.2769 3 N 0.0109 0.8462 0.1429 4 I 0.0080 0.9131 0.0789 5 Y 0.0062 0.9394 0.0544 6 I 0.0055 0.9498 0.0447 7 Y 0.0049 0.9565 0.0386 8 L 0.0047 0.9584 0.0369 9 S 0.0047 0.9590 0.0364 10 L 0.0047 0.9588 0.0366 11 L 0.0047 0.9584 0.0369 12 A 0.0047 0.9575 0.0378 13 V 0.0055 0.9552 0.0393 14 I 0.0071 0.9501 0.0428 15 V 0.0107 0.9330 0.0563 16 L 0.0187 0.8724 0.1089 17 G 0.0419 0.7048 0.2533 18 T 0.0624 0.4281 0.5095 19 A 0.0507 0.2283 0.7210 20 C 0.0700 0.1409 0.7891 21 N 0.0330 0.1762 0.7908 22 N 0.0622 0.4234 0.5143 23 E 0.0316 0.6666 0.3018 24 W 0.0404 0.6578 0.3018 25 E 0.0389 0.7195 0.2417 26 D 0.0346 0.8044 0.1610 27 E 0.0583 0.7818 0.1599 28 Q 0.0797 0.7298 0.1905 29 Y 0.1328 0.6608 0.2065 30 E 0.1809 0.5591 0.2600 31 Q 0.2619 0.4268 0.3113 32 Y 0.4653 0.3123 0.2224 33 V 0.5977 0.2183 0.1839 34 S 0.6608 0.1816 0.1576 35 F 0.6532 0.1562 0.1906 36 K 0.5853 0.1280 0.2867 37 A 0.4360 0.0688 0.4952 38 P 0.3312 0.0600 0.6088 39 I 0.2302 0.0982 0.6716 40 A 0.1844 0.1075 0.7082 41 S 0.1490 0.1424 0.7086 42 G 0.1960 0.1016 0.7025 43 S 0.3238 0.0750 0.6012 44 D 0.3967 0.0707 0.5326 45 G 0.5350 0.0473 0.4177 46 V 0.7200 0.0169 0.2632 47 T 0.7800 0.0178 0.2023 48 T 0.8281 0.0091 0.1627 49 I 0.8555 0.0077 0.1368 50 Y 0.8777 0.0053 0.1170 51 V 0.8654 0.0055 0.1291 52 R 0.8616 0.0051 0.1333 53 Y 0.8159 0.0071 0.1771 54 K 0.4819 0.0129 0.5052 55 D 0.0925 0.0693 0.8382 56 N 0.0471 0.0314 0.9215 57 G 0.0834 0.0377 0.8789 58 K 0.5241 0.0127 0.4631 59 V 0.8610 0.0048 0.1343 60 T 0.8917 0.0049 0.1034 61 Y 0.9029 0.0040 0.0931 62 Q 0.9018 0.0036 0.0946 63 L 0.8857 0.0046 0.1098 64 P 0.8826 0.0042 0.1131 65 I 0.9103 0.0039 0.0858 66 I 0.9136 0.0044 0.0820 67 V 0.8794 0.0076 0.1130 68 S 0.6402 0.0260 0.3338 69 G 0.4007 0.0270 0.5723 70 S 0.3198 0.0435 0.6367 71 T 0.2855 0.0353 0.6792 72 V 0.1666 0.1046 0.7289 73 N 0.0963 0.1051 0.7986 74 S 0.0852 0.1368 0.7779 75 Q 0.1111 0.1104 0.7785 76 D 0.2584 0.0406 0.7010 77 R 0.6267 0.0147 0.3586 78 D 0.8424 0.0062 0.1514 79 I 0.8857 0.0057 0.1087 80 H 0.8979 0.0049 0.0972 81 I 0.8671 0.0092 0.1237 82 A 0.8099 0.0121 0.1781 83 V 0.4996 0.0203 0.4801 84 D 0.1480 0.0191 0.8330 85 K 0.0069 0.6366 0.3566 86 D 0.0058 0.6655 0.3287 87 T 0.0076 0.8586 0.1338 88 L 0.0079 0.9077 0.0844 89 K 0.0064 0.9298 0.0638 90 T 0.0080 0.9337 0.0583 91 L 0.0138 0.9169 0.0692 92 N 0.0182 0.8792 0.1025 93 I 0.0116 0.8544 0.1339 94 E 0.0162 0.7981 0.1857 95 R 0.0412 0.6562 0.3025 96 F 0.0769 0.4183 0.5048 97 S 0.0961 0.3529 0.5510 98 L 0.0885 0.3466 0.5649 99 Y 0.0888 0.2250 0.6862 100 R 0.0646 0.3949 0.5404 101 P 0.0522 0.4635 0.4843 102 E 0.0991 0.4612 0.4397 103 L 0.1700 0.3719 0.4581 104 W 0.2724 0.2786 0.4490 105 Y 0.4410 0.2619 0.2971 106 T 0.5174 0.2180 0.2646 107 E 0.4559 0.2323 0.3119 108 M 0.2474 0.0991 0.6535 109 E 0.1044 0.1614 0.7342 110 E 0.0344 0.4214 0.5443 111 D 0.0512 0.4017 0.5471 112 K 0.1896 0.2823 0.5282 113 Y 0.5037 0.0341 0.4623 114 E 0.5888 0.0227 0.3885 115 F 0.4203 0.0327 0.5470 116 P 0.1804 0.0659 0.7537 117 E 0.1421 0.0893 0.7686 118 T 0.3851 0.0421 0.5728 119 V 0.6948 0.0130 0.2922 120 H 0.8122 0.0062 0.1816 121 I 0.6579 0.0087 0.3334 122 P 0.2275 0.0181 0.7544 123 A 0.0570 0.0667 0.8763 124 G 0.0558 0.0538 0.8904 125 S 0.2836 0.0331 0.6833 126 C 0.6143 0.0159 0.3698 127 V 0.7149 0.0270 0.2582 128 E 0.7541 0.0201 0.2259 129 L 0.8009 0.0166 0.1825 130 L 0.7574 0.0083 0.2343 131 N 0.7150 0.0068 0.2782 132 I 0.7756 0.0056 0.2188 133 D 0.8072 0.0045 0.1884 134 F 0.7310 0.0066 0.2624 135 N 0.4374 0.0116 0.5510 136 L 0.0702 0.2710 0.6588 137 Q 0.0301 0.2369 0.7330 138 D 0.0532 0.2260 0.7208 139 I 0.2258 0.0528 0.7215 140 D 0.1805 0.0390 0.7805 141 M 0.0504 0.2528 0.6968 142 L 0.0503 0.2544 0.6953 143 E 0.1064 0.2273 0.6663 144 K 0.2856 0.0811 0.6333 145 W 0.6276 0.0351 0.3373 146 V 0.7381 0.0148 0.2471 147 L 0.6736 0.0080 0.3183 148 P 0.6560 0.0065 0.3375 149 L 0.8349 0.0042 0.1609 150 T 0.8784 0.0049 0.1168 151 I 0.8801 0.0040 0.1159 152 V 0.7241 0.0320 0.2439 153 D 0.4085 0.0197 0.5718 154 D 0.1417 0.0389 0.8194 155 G 0.0650 0.0892 0.8459 156 S 0.0843 0.0862 0.8294 157 Y 0.1508 0.0838 0.7654 158 A 0.3147 0.0876 0.5978 159 Y 0.4956 0.0815 0.4229 160 Q 0.5163 0.0599 0.4238 161 S 0.4304 0.0753 0.4943 162 H 0.2205 0.0577 0.7218 163 P 0.0478 0.2630 0.6892 164 R 0.0610 0.2136 0.7254 165 K 0.0803 0.2323 0.6874 166 N 0.1590 0.1980 0.6430 167 Y 0.3707 0.2259 0.4034 168 A 0.5864 0.1733 0.2403 169 K 0.7093 0.1436 0.1471 170 A 0.7607 0.1218 0.1175 171 L 0.7537 0.1265 0.1197 172 L 0.7241 0.1169 0.1590 173 K 0.7007 0.0924 0.2070 174 V 0.6581 0.0488 0.2930 175 V 0.5820 0.0280 0.3899 176 P 0.5669 0.0360 0.3971 177 F 0.5023 0.0749 0.4228 178 N 0.3348 0.0541 0.6111 179 N 0.1396 0.1360 0.7243 180 Y 0.1282 0.1137 0.7581 181 S 0.2051 0.0952 0.6997 182 G 0.2310 0.0737 0.6953 183 S 0.3653 0.0742 0.5605 184 Y 0.4679 0.0655 0.4666 185 T 0.3546 0.0687 0.5768 186 A 0.2825 0.1212 0.5962 187 S 0.3091 0.1336 0.5573 188 S 0.4696 0.0802 0.4502 189 M 0.6579 0.0369 0.3053 190 K 0.7891 0.0207 0.1902 191 V 0.8264 0.0186 0.1551 192 Y 0.8330 0.0169 0.1502 193 T 0.8089 0.0210 0.1701 194 Y 0.6564 0.0410 0.3027 195 I 0.3610 0.0770 0.5619 196 N 0.1567 0.1094 0.7339 197 G 0.1139 0.0875 0.7986 198 K 0.1038 0.0709 0.8253 199 P 0.1401 0.0679 0.7919 200 D 0.1744 0.0762 0.7494 201 T 0.1690 0.0695 0.7616 202 N 0.2224 0.0509 0.7267 203 A 0.3189 0.0707 0.6103 204 R 0.5364 0.0613 0.4023 205 T 0.6549 0.0514 0.2938 206 T 0.7060 0.0487 0.2453 207 D 0.7340 0.0404 0.2256 208 K 0.8038 0.0226 0.1737 209 R 0.8112 0.0200 0.1688 210 T 0.8105 0.0149 0.1747 211 G 0.7742 0.0180 0.2079 212 Y 0.8021 0.0117 0.1862 213 V 0.8231 0.0089 0.1680 214 V 0.7224 0.0174 0.2602 215 D 0.4709 0.0188 0.5103 216 N 0.0929 0.1650 0.7420 217 N 0.1327 0.1241 0.7432 218 S 0.6348 0.0680 0.2972 219 I 0.8131 0.0370 0.1499 220 F 0.8801 0.0215 0.0984 221 F 0.8514 0.0343 0.1143 222 Y 0.8032 0.0470 0.1498 223 A 0.6451 0.0835 0.2714 224 G 0.5284 0.0737 0.3979 225 L 0.5849 0.0673 0.3478 226 I 0.5534 0.0815 0.3651 227 N 0.3608 0.1054 0.5338 228 E 0.0799 0.4634 0.4566 229 D 0.0474 0.4802 0.4723 230 M 0.0500 0.5535 0.3966 231 D 0.0559 0.6176 0.3265 232 K 0.0914 0.5607 0.3479 233 D 0.0997 0.5628 0.3375 234 M 0.1317 0.4673 0.4010 235 R 0.1590 0.2957 0.5453 236 K 0.2116 0.1344 0.6539 237 K 0.3759 0.0560 0.5680 238 Y 0.7228 0.0189 0.2583 239 K 0.8399 0.0122 0.1479 240 I 0.8807 0.0076 0.1117 241 N 0.8914 0.0052 0.1034 242 V 0.8289 0.0069 0.1642 243 H 0.6261 0.0123 0.3616 244 F 0.2612 0.0536 0.6853 245 K 0.1090 0.0516 0.8394 246 E 0.0911 0.0866 0.8223 247 D 0.1383 0.0730 0.7887 248 G 0.2900 0.0522 0.6578 249 T 0.6262 0.0201 0.3537 250 L 0.8153 0.0091 0.1756 251 D 0.8584 0.0079 0.1337 252 M 0.8303 0.0100 0.1596 253 K 0.8036 0.0128 0.1836 254 Q 0.7124 0.0221 0.2655 255 D 0.5612 0.0299 0.4089 256 D 0.3501 0.0400 0.6099 257 P 0.1386 0.1178 0.7436 258 S 0.1088 0.1100 0.7812 259 N 0.0696 0.1521 0.7783 260 E 0.1150 0.1237 0.7613 261 M 0.3398 0.0764 0.5838 262 E 0.4693 0.0473 0.4834 263 F 0.6461 0.0390 0.3148 264 E 0.6570 0.0368 0.3062 265 L 0.5935 0.0494 0.3571 266 I 0.3356 0.0739 0.5905 267 G 0.1633 0.0577 0.7789 268 T 0.1479 0.0420 0.8101 269 P 0.1874 0.0735 0.7391 270 T 0.3712 0.0488 0.5800 271 Y 0.6159 0.0221 0.3620 272 S 0.7058 0.0204 0.2738 273 S 0.7454 0.0379 0.2167 274 T 0.7202 0.0561 0.2236 275 S 0.7049 0.0669 0.2283 276 V 0.6765 0.0603 0.2632 277 M 0.5339 0.0521 0.4140 278 D 0.1896 0.0454 0.7650 279 A 0.0464 0.1461 0.8075 280 T 0.0525 0.0968 0.8507 281 R 0.1126 0.0570 0.8304 282 P 0.1968 0.1223 0.6809 283 Y 0.5306 0.1023 0.3670 284 L 0.7435 0.0541 0.2024 285 E 0.8111 0.0288 0.1601 286 R 0.8197 0.0153 0.1650 287 R 0.8710 0.0097 0.1193 288 Y 0.8997 0.0053 0.0950 289 V 0.9042 0.0050 0.0908 290 Q 0.9002 0.0047 0.0951 291 I 0.8276 0.0081 0.1642 292 M 0.6770 0.0134 0.3096 293 F 0.4666 0.0445 0.4889 294 E 0.4866 0.0388 0.4747 295 Y 0.4902 0.0302 0.4796 296 D 0.4656 0.0249 0.5095 297 F 0.3942 0.0502 0.5556 298 Q 0.2497 0.0977 0.6526 299 D 0.2632 0.0740 0.6628 300 F 0.2861 0.1081 0.6058 301 T 0.3320 0.0719 0.5961 302 Y 0.3534 0.0590 0.5876 303 G 0.1800 0.0456 0.7745 304 G 0.0741 0.0998 0.8261 305 S 0.0597 0.0717 0.8686 306 G 0.1002 0.0698 0.8300 307 T 0.2599 0.0563 0.6838 308 E 0.3829 0.0528 0.5644 309 V 0.4677 0.0334 0.4989 310 I 0.5864 0.0127 0.4009 311 P 0.6737 0.0085 0.3177 312 I 0.7664 0.0070 0.2266 313 K 0.7824 0.0045 0.2131 314 Y 0.8391 0.0053 0.1556 315 R 0.8998 0.0034 0.0968 316 V 0.9021 0.0041 0.0937 317 A 0.8352 0.0239 0.1408 318 G 0.8247 0.0099 0.1655 319 S 0.8552 0.0089 0.1358 320 M 0.8609 0.0116 0.1275 321 T 0.8636 0.0155 0.1209 322 L 0.8265 0.0329 0.1406 323 L 0.8420 0.0297 0.1283 324 R 0.6900 0.0748 0.2352 325 N 0.5445 0.0927 0.3628 326 I 0.3991 0.1195 0.4814 327 N 0.2933 0.0875 0.6192 328 T 0.2756 0.0781 0.6463 329 Q 0.3060 0.0583 0.6357 330 I 0.2142 0.0351 0.7507 331 P 0.1098 0.0263 0.8639 332 D 0.0703 0.1403 0.7894 333 E 0.0132 0.7147 0.2721 334 D 0.0132 0.7947 0.1921 335 Q 0.0268 0.7438 0.2293 336 Q 0.0491 0.6939 0.2571 337 I 0.0681 0.5592 0.3727 338 E 0.0635 0.4089 0.5276 339 W 0.0328 0.0800 0.8872