# This file is the result of combining several RDB files, specifically # T0320.t04.dssp-ebghstl.rdb (weight 1.53986) # T0320.t04.stride-ebghtl.rdb (weight 1.24869) # T0320.t04.str2.rdb (weight 1.54758) # T0320.t04.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 T0320.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0320 # 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 T0320.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 1874 # # ============================================ # Comments from T0320.t04.stride-ebghtl.rdb # ============================================ # TARGET T0320 # 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 T0320.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 1874 # # ============================================ # Comments from T0320.t04.str2.rdb # ============================================ # TARGET T0320 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0320.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 1874 # # ============================================ # Comments from T0320.t04.alpha.rdb # ============================================ # TARGET T0320 # 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 T0320.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 1874 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0824 0.1494 0.7681 2 Q 0.1284 0.1521 0.7195 3 L 0.1670 0.1505 0.6824 4 S 0.1610 0.1167 0.7223 5 K 0.1957 0.1934 0.6109 6 A 0.3458 0.2153 0.4389 7 A 0.5471 0.1654 0.2875 8 E 0.5968 0.1395 0.2637 9 M 0.5209 0.1107 0.3684 10 C 0.2845 0.0709 0.6447 11 Y 0.2102 0.2065 0.5833 12 E 0.3088 0.2111 0.4801 13 I 0.3880 0.2018 0.4102 14 T 0.3439 0.1752 0.4809 15 N 0.2636 0.1356 0.6009 16 S 0.1834 0.1298 0.6869 17 Y 0.1270 0.2999 0.5731 18 L 0.0956 0.3379 0.5665 19 H 0.1063 0.3155 0.5782 20 I 0.0900 0.5039 0.4060 21 D 0.1298 0.5512 0.3190 22 Q 0.0806 0.6207 0.2988 23 K 0.0434 0.7023 0.2542 24 S 0.0282 0.7924 0.1794 25 Q 0.0151 0.8291 0.1557 26 I 0.0153 0.8502 0.1345 27 I 0.0095 0.8974 0.0932 28 A 0.0050 0.9373 0.0576 29 S 0.0051 0.9345 0.0604 30 T 0.0054 0.9342 0.0604 31 Q 0.0052 0.9431 0.0517 32 E 0.0048 0.9494 0.0458 33 A 0.0048 0.9457 0.0494 34 I 0.0055 0.9208 0.0737 35 R 0.0077 0.8638 0.1285 36 L 0.0135 0.8512 0.1353 37 T 0.0169 0.7485 0.2346 38 R 0.0048 0.9502 0.0450 39 K 0.0047 0.9566 0.0386 40 Y 0.0047 0.9583 0.0370 41 L 0.0047 0.9587 0.0366 42 L 0.0047 0.9602 0.0351 43 S 0.0047 0.9600 0.0353 44 E 0.0048 0.9587 0.0365 45 I 0.0051 0.9544 0.0405 46 F 0.0058 0.9402 0.0540 47 V 0.0069 0.8994 0.0937 48 R 0.0128 0.7338 0.2534 49 W 0.0721 0.4467 0.4812 50 S 0.0795 0.1472 0.7733 51 P 0.0232 0.2942 0.6826 52 L 0.0244 0.1990 0.7766 53 N 0.0530 0.0710 0.8760 54 G 0.1146 0.0289 0.8565 55 E 0.5709 0.0087 0.4204 56 I 0.9080 0.0033 0.0886 57 S 0.9293 0.0035 0.0672 58 F 0.9308 0.0033 0.0658 59 S 0.9203 0.0042 0.0755 60 Y 0.8435 0.0093 0.1472 61 N 0.5425 0.0173 0.4402 62 G 0.1704 0.0391 0.7905 63 G 0.1067 0.0823 0.8110 64 K 0.0544 0.3714 0.5741 65 D 0.0276 0.6271 0.3453 66 C 0.0079 0.9223 0.0698 67 Q 0.0052 0.9550 0.0399 68 V 0.0047 0.9606 0.0347 69 L 0.0047 0.9608 0.0346 70 L 0.0047 0.9610 0.0343 71 L 0.0047 0.9610 0.0343 72 L 0.0047 0.9596 0.0357 73 Y 0.0050 0.9529 0.0421 74 L 0.0066 0.9278 0.0656 75 S 0.0088 0.7821 0.2091 76 C 0.0286 0.4406 0.5308 77 L 0.0589 0.0532 0.8879 78 W 0.0726 0.0351 0.8923 79 E 0.2629 0.0536 0.6835 80 Y 0.8586 0.0071 0.1343 81 F 0.9201 0.0038 0.0762 82 F 0.9247 0.0036 0.0716 83 I 0.8827 0.0073 0.1100 84 K 0.5991 0.0101 0.3908 85 A 0.2181 0.0402 0.7418 86 Q 0.0872 0.0837 0.8291 87 N 0.0667 0.1128 0.8205 88 S 0.0691 0.1359 0.7949 89 Q 0.0731 0.1428 0.7841 90 F 0.0698 0.0851 0.8452 91 D 0.0582 0.1592 0.7826 92 F 0.0295 0.5257 0.4449 93 E 0.0399 0.6444 0.3156 94 F 0.0516 0.6666 0.2817 95 Q 0.0593 0.5988 0.3419 96 S 0.0561 0.5681 0.3757 97 F 0.0507 0.5700 0.3792 98 P 0.0256 0.7802 0.1942 99 M 0.0255 0.8423 0.1323 100 Q 0.0188 0.8408 0.1404 101 R 0.0213 0.8097 0.1690 102 L 0.0609 0.6797 0.2594 103 P 0.0259 0.7874 0.1867 104 T 0.0576 0.7239 0.2185 105 V 0.0986 0.4177 0.4837 106 F 0.0819 0.0243 0.8938 107 I 0.1349 0.0087 0.8563 108 D 0.3519 0.0105 0.6376 109 Q 0.6783 0.0425 0.2792 110 E 0.8225 0.0374 0.1401 111 E 0.8342 0.0185 0.1472 112 T 0.5808 0.0418 0.3774 113 F 0.2243 0.0155 0.7602 114 P 0.0633 0.1154 0.8213 115 T 0.0565 0.1440 0.7996 116 L 0.0237 0.6468 0.3294 117 E 0.0133 0.7770 0.2097 118 N 0.0127 0.8356 0.1517 119 F 0.0161 0.8819 0.1020 120 V 0.0131 0.9124 0.0745 121 L 0.0086 0.9341 0.0573 122 E 0.0090 0.9276 0.0634 123 T 0.0101 0.9132 0.0767 124 S 0.0131 0.8902 0.0967 125 E 0.0159 0.8622 0.1219 126 R 0.0243 0.8233 0.1524 127 Y 0.0466 0.6740 0.2794 128 C 0.0813 0.3952 0.5236 129 L 0.0368 0.6679 0.2954 130 S 0.0368 0.7154 0.2478 131 L 0.0400 0.7006 0.2594 132 Y 0.0910 0.5743 0.3347 133 E 0.1209 0.4619 0.4172 134 S 0.1319 0.3567 0.5114 135 Q 0.1503 0.2790 0.5707 136 R 0.1028 0.3044 0.5928 137 Q 0.0855 0.2745 0.6401 138 S 0.1022 0.2340 0.6638 139 G 0.1037 0.1356 0.7608 140 A 0.2337 0.1686 0.5977 141 S 0.4630 0.1811 0.3559 142 V 0.4477 0.2103 0.3420 143 N 0.3729 0.2185 0.4086 144 M 0.1359 0.4544 0.4096 145 A 0.0497 0.4955 0.4548 146 D 0.0074 0.8839 0.1087 147 A 0.0076 0.8948 0.0976 148 F 0.0066 0.9271 0.0662 149 R 0.0050 0.9521 0.0429 150 D 0.0049 0.9496 0.0455 151 F 0.0053 0.9419 0.0528 152 I 0.0053 0.9054 0.0893 153 K 0.0062 0.7951 0.1987 154 I 0.0141 0.5892 0.3967 155 Y 0.0800 0.0565 0.8634 156 P 0.0118 0.1760 0.8122 157 E 0.0203 0.0881 0.8915 158 T 0.1827 0.0363 0.7810 159 E 0.2784 0.0550 0.6666 160 A 0.9061 0.0045 0.0893 161 I 0.9286 0.0037 0.0677 162 V 0.9223 0.0053 0.0723 163 I 0.8549 0.0146 0.1305 164 G 0.6367 0.0199 0.3434 165 I 0.4128 0.0349 0.5523 166 R 0.2206 0.0391 0.7403 167 H 0.1051 0.1023 0.7926 168 T 0.0641 0.0803 0.8556 169 D 0.0693 0.0848 0.8459 170 P 0.0423 0.2364 0.7214 171 F 0.0626 0.2921 0.6453 172 G 0.0941 0.2726 0.6334 173 E 0.1590 0.2743 0.5667 174 A 0.2466 0.2212 0.5322 175 L 0.2806 0.1522 0.5671 176 K 0.2820 0.0639 0.6541 177 P 0.3042 0.0873 0.6085 178 I 0.4287 0.1399 0.4315 179 Q 0.5285 0.1179 0.3536 180 R 0.4627 0.1071 0.4301 181 T 0.2670 0.0901 0.6429 182 D 0.1019 0.0485 0.8495 183 S 0.0198 0.1223 0.8578 184 N 0.0304 0.0836 0.8860 185 W 0.0780 0.0734 0.8486 186 P 0.0403 0.1640 0.7957 187 D 0.0685 0.1662 0.7653 188 F 0.3061 0.1169 0.5770 189 M 0.5912 0.0757 0.3331 190 R 0.7736 0.0401 0.1863 191 L 0.7091 0.0505 0.2404 192 Q 0.5869 0.0378 0.3753 193 P 0.3522 0.1054 0.5424 194 L 0.2301 0.2205 0.5494 195 L 0.1868 0.1985 0.6147 196 H 0.1674 0.0891 0.7435 197 W 0.2048 0.0329 0.7624 198 D 0.1035 0.0293 0.8672 199 L 0.0049 0.9263 0.0688 200 T 0.0047 0.9462 0.0492 201 N 0.0047 0.9569 0.0383 202 I 0.0047 0.9608 0.0345 203 W 0.0047 0.9609 0.0345 204 S 0.0047 0.9614 0.0339 205 F 0.0047 0.9607 0.0346 206 L 0.0048 0.9580 0.0372 207 L 0.0052 0.9500 0.0448 208 Y 0.0073 0.9108 0.0819 209 S 0.0470 0.5148 0.4381 210 N 0.0343 0.0327 0.9330 211 E 0.0612 0.0117 0.9270 212 P 0.1286 0.0400 0.8314 213 I 0.2286 0.1317 0.6397 214 C 0.2022 0.1806 0.6172 215 G 0.1448 0.2521 0.6032 216 L 0.1646 0.2470 0.5884 217 Y 0.1177 0.1772 0.7051 218 G 0.0940 0.1024 0.8037 219 K 0.1130 0.0606 0.8264 220 G 0.1293 0.0537 0.8169 221 F 0.2396 0.0379 0.7226 222 T 0.2868 0.0446 0.6686 223 S 0.2243 0.0412 0.7345 224 I 0.1469 0.1152 0.7379 225 G 0.1174 0.0779 0.8047 226 G 0.1485 0.0738 0.7777 227 I 0.1616 0.1022 0.7362 228 N 0.2177 0.1212 0.6611 229 N 0.2117 0.0946 0.6937 230 S 0.1979 0.0804 0.7217 231 L 0.1841 0.0340 0.7819 232 P 0.1554 0.0463 0.7983 233 N 0.1199 0.0317 0.8484 234 P 0.0673 0.1540 0.7787 235 H 0.1171 0.2241 0.6588 236 L 0.1819 0.2258 0.5922 237 R 0.1926 0.1529 0.6545 238 K 0.2085 0.1708 0.6208 239 D 0.1250 0.1284 0.7467 240 S 0.0612 0.1784 0.7604 241 N 0.0626 0.1251 0.8123 242 N 0.0967 0.0947 0.8085 243 P 0.0385 0.2814 0.6801 244 A 0.0821 0.3863 0.5316 245 L 0.1149 0.4953 0.3898 246 H 0.0915 0.5303 0.3782 247 F 0.1102 0.5263 0.3634 248 E 0.0734 0.6977 0.2288 249 W 0.0377 0.8501 0.1122 250 E 0.0245 0.8938 0.0817 251 I 0.0243 0.9035 0.0722 252 I 0.0264 0.9040 0.0695 253 H 0.0186 0.8889 0.0924 254 A 0.0217 0.8215 0.1567 255 F 0.0582 0.5896 0.3522 256 G 0.0784 0.2971 0.6245 257 K 0.1230 0.3166 0.5604 258 D 0.1047 0.2783 0.6170 259 A 0.0446 0.2948 0.6607 260 E 0.0453 0.1848 0.7699 261 G 0.0661 0.1344 0.7994 262 E 0.1729 0.1066 0.7205 263 R 0.2871 0.1182 0.5947 264 S 0.1879 0.3078 0.5043 265 S 0.1040 0.5339 0.3621 266 A 0.1568 0.5129 0.3303 267 I 0.2249 0.4129 0.3622 268 N 0.1973 0.2427 0.5600 269 T 0.1369 0.1513 0.7118 270 S 0.1304 0.0660 0.8035 271 P 0.1299 0.1321 0.7380 272 I 0.3918 0.1378 0.4705 273 S 0.5997 0.1191 0.2812 274 V 0.6190 0.1065 0.2745 275 V 0.5008 0.1069 0.3923 276 D 0.2978 0.1089 0.5933 277 K 0.1692 0.2760 0.5547 278 E 0.1461 0.3736 0.4804 279 R 0.1615 0.3877 0.4507 280 F 0.1968 0.3909 0.4123 281 S 0.2404 0.3970 0.3626 282 K 0.2600 0.3661 0.3739 283 Y 0.2542 0.2955 0.4502 284 H 0.1657 0.2682 0.5661 285 D 0.0806 0.2750 0.6444 286 N 0.0623 0.2175 0.7202 287 Y 0.1004 0.1057 0.7939 288 Y 0.1159 0.0448 0.8393 289 P 0.1149 0.0591 0.8260 290 G 0.4214 0.0422 0.5365 291 W 0.7547 0.0190 0.2262 292 Y 0.8002 0.0142 0.1855 293 L 0.5968 0.0189 0.3843 294 V 0.2725 0.0419 0.6855 295 D 0.0933 0.1557 0.7510 296 D 0.0237 0.5186 0.4577 297 T 0.0504 0.6792 0.2704 298 L 0.1264 0.7215 0.1521 299 E 0.1735 0.6554 0.1711 300 R 0.2136 0.5768 0.2096 301 A 0.1638 0.5500 0.2861 302 G 0.1914 0.3659 0.4427 303 R 0.2959 0.2178 0.4863 304 I 0.3778 0.1722 0.4500 305 K 0.2626 0.1367 0.6007 306 N 0.1009 0.0530 0.8461