# This file is the result of combining several RDB files, specifically # T0136.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0136.t2k.stride-ebghtl.rdb (weight 1.24869) # T0136.t2k.str.rdb (weight 1.53983) # T0136.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 T0136.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0136 # 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 T0136.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 253 # # ============================================ # Comments from T0136.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0136 # 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 T0136.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 253 # # ============================================ # Comments from T0136.t2k.str.rdb # ============================================ # TARGET T0136 # 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 T0136.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 253 # # ============================================ # Comments from T0136.t2k.alpha.rdb # ============================================ # TARGET T0136 # 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 T0136.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 253 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0682 0.0681 0.8637 2 L 0.1648 0.1329 0.7023 3 S 0.1707 0.1527 0.6766 4 F 0.1781 0.1897 0.6322 5 L 0.1820 0.0974 0.7206 6 P 0.1380 0.1188 0.7432 7 Q 0.0812 0.2372 0.6816 8 N 0.0650 0.2084 0.7266 9 N 0.0687 0.1703 0.7610 10 T 0.0540 0.2175 0.7286 11 E 0.0552 0.2390 0.7058 12 E 0.0616 0.2959 0.6426 13 A 0.0604 0.3067 0.6329 14 S 0.0735 0.3714 0.5551 15 F 0.0784 0.4625 0.4591 16 V 0.0648 0.4417 0.4935 17 N 0.0586 0.4566 0.4848 18 P 0.0387 0.4694 0.4919 19 N 0.0457 0.4395 0.5148 20 N 0.0478 0.4116 0.5406 21 D 0.0430 0.4344 0.5226 22 V 0.0476 0.4353 0.5171 23 S 0.0469 0.4071 0.5460 24 P 0.0427 0.3248 0.6325 25 N 0.0418 0.2877 0.6706 26 T 0.0478 0.2698 0.6824 27 E 0.0579 0.3652 0.5769 28 L 0.0748 0.4535 0.4717 29 R 0.1076 0.4285 0.4640 30 D 0.1763 0.3608 0.4629 31 I 0.2355 0.2785 0.4859 32 V 0.2651 0.1804 0.5544 33 P 0.2033 0.1696 0.6271 34 I 0.1246 0.1762 0.6992 35 D 0.0752 0.1370 0.7878 36 G 0.0570 0.1341 0.8089 37 K 0.0413 0.1510 0.8077 38 K 0.0568 0.0834 0.8597 39 G 0.0966 0.0468 0.8566 40 Y 0.1566 0.0419 0.8016 41 D 0.1307 0.0357 0.8336 42 V 0.0062 0.9165 0.0773 43 R 0.0045 0.9474 0.0481 44 D 0.0047 0.9515 0.0438 45 V 0.0047 0.9494 0.0459 46 I 0.0059 0.9244 0.0697 47 A 0.0093 0.8867 0.1040 48 K 0.0145 0.8036 0.1819 49 I 0.0332 0.6947 0.2721 50 V 0.1270 0.3382 0.5348 51 D 0.0736 0.0736 0.8529 52 W 0.0305 0.1676 0.8019 53 G 0.0360 0.1166 0.8475 54 D 0.2053 0.1386 0.6561 55 Y 0.4074 0.1660 0.4265 56 L 0.4485 0.1710 0.3805 57 E 0.4306 0.1761 0.3933 58 V 0.3114 0.1842 0.5044 59 K 0.2730 0.1793 0.5477 60 A 0.1605 0.2318 0.6076 61 G 0.1374 0.1764 0.6862 62 Y 0.0994 0.1517 0.7489 63 A 0.0916 0.1015 0.8069 64 T 0.0402 0.1179 0.8419 65 N 0.0957 0.0610 0.8433 66 L 0.5334 0.0138 0.4528 67 V 0.8269 0.0061 0.1670 68 T 0.8650 0.0139 0.1211 69 A 0.8982 0.0083 0.0935 70 F 0.8925 0.0136 0.0939 71 A 0.8937 0.0077 0.0987 72 R 0.9032 0.0067 0.0901 73 V 0.8213 0.0235 0.1552 74 N 0.0926 0.0342 0.8733 75 G 0.0425 0.0499 0.9075 76 R 0.6097 0.0105 0.3797 77 S 0.8345 0.0040 0.1614 78 V 0.9074 0.0064 0.0862 79 G 0.9296 0.0040 0.0664 80 I 0.9315 0.0036 0.0649 81 V 0.9122 0.0077 0.0802 82 A 0.8540 0.0102 0.1358 83 N 0.5503 0.0246 0.4251 84 Q 0.1646 0.0230 0.8124 85 P 0.0789 0.1436 0.7776 86 S 0.1654 0.1687 0.6659 87 V 0.3332 0.1617 0.5050 88 M 0.3234 0.1221 0.5544 89 S 0.2742 0.1185 0.6074 90 G 0.2186 0.0730 0.7083 91 C 0.2672 0.0670 0.6658 92 L 0.1715 0.0653 0.7632 93 D 0.0707 0.0480 0.8813 94 I 0.0149 0.7288 0.2562 95 N 0.0073 0.8614 0.1313 96 A 0.0075 0.9166 0.0759 97 S 0.0047 0.9455 0.0498 98 D 0.0046 0.9528 0.0426 99 K 0.0045 0.9544 0.0411 100 A 0.0044 0.9589 0.0367 101 A 0.0044 0.9604 0.0353 102 E 0.0044 0.9606 0.0350 103 F 0.0044 0.9600 0.0356 104 V 0.0044 0.9599 0.0357 105 N 0.0044 0.9582 0.0374 106 F 0.0044 0.9572 0.0384 107 C 0.0046 0.9514 0.0440 108 D 0.0053 0.9298 0.0649 109 S 0.0062 0.8714 0.1224 110 F 0.0456 0.4500 0.5044 111 N 0.0384 0.0335 0.9281 112 I 0.0718 0.0095 0.9187 113 P 0.2587 0.0085 0.7328 114 L 0.8610 0.0036 0.1354 115 V 0.9218 0.0043 0.0739 116 Q 0.9295 0.0037 0.0669 117 L 0.9206 0.0042 0.0752 118 V 0.8456 0.0103 0.1441 119 D 0.4661 0.0239 0.5100 120 V 0.1434 0.0604 0.7963 121 P 0.0696 0.1095 0.8209 122 G 0.0853 0.1370 0.7776 123 F 0.1410 0.1122 0.7468 124 L 0.1685 0.1224 0.7091 125 P 0.0813 0.2068 0.7119 126 G 0.0519 0.3019 0.6462 127 V 0.0310 0.7531 0.2159 128 Q 0.0221 0.8429 0.1351 129 Q 0.0140 0.8743 0.1117 130 E 0.0147 0.8590 0.1263 131 Y 0.0107 0.8535 0.1359 132 G 0.0148 0.8040 0.1812 133 G 0.0087 0.8061 0.1852 134 I 0.0066 0.8870 0.1064 135 I 0.0048 0.9333 0.0619 136 R 0.0045 0.9443 0.0512 137 H 0.0044 0.9485 0.0471 138 G 0.0044 0.9535 0.0421 139 A 0.0044 0.9573 0.0383 140 K 0.0044 0.9567 0.0389 141 M 0.0044 0.9550 0.0406 142 L 0.0044 0.9551 0.0404 143 Y 0.0050 0.9479 0.0471 144 A 0.0046 0.9478 0.0476 145 Y 0.0054 0.9336 0.0610 146 S 0.0083 0.8664 0.1253 147 E 0.0151 0.5819 0.4030 148 A 0.0600 0.2083 0.7317 149 T 0.0634 0.0718 0.8648 150 V 0.1330 0.0143 0.8527 151 P 0.2083 0.0096 0.7822 152 K 0.8275 0.0097 0.1628 153 I 0.9272 0.0035 0.0693 154 T 0.9285 0.0040 0.0675 155 V 0.9273 0.0038 0.0690 156 V 0.8834 0.0064 0.1101 157 L 0.6330 0.0198 0.3472 158 R 0.2805 0.0267 0.6928 159 K 0.1148 0.0986 0.7867 160 A 0.1163 0.1058 0.7779 161 Y 0.1173 0.1321 0.7506 162 G 0.1112 0.1220 0.7667 163 G 0.1458 0.2216 0.6325 164 S 0.2204 0.3063 0.4733 165 Y 0.3060 0.3409 0.3531 166 L 0.3266 0.3341 0.3393 167 A 0.3479 0.2833 0.3689 168 M 0.2563 0.2586 0.4851 169 C 0.1424 0.2255 0.6322 170 N 0.0684 0.4385 0.4931 171 R 0.0380 0.5029 0.4590 172 D 0.0588 0.4186 0.5226 173 L 0.1044 0.2388 0.6568 174 G 0.1153 0.0771 0.8075 175 A 0.1319 0.0554 0.8127 176 D 0.2241 0.0676 0.7082 177 A 0.8080 0.0158 0.1761 178 V 0.8788 0.0085 0.1127 179 Y 0.8950 0.0079 0.0971 180 A 0.8519 0.0082 0.1399 181 W 0.4625 0.0145 0.5230 182 P 0.0622 0.0889 0.8489 183 S 0.0536 0.0550 0.8914 184 A 0.3162 0.0258 0.6581 185 E 0.6569 0.0217 0.3215 186 I 0.8935 0.0081 0.0984 187 A 0.9047 0.0060 0.0894 188 V 0.8790 0.0130 0.1080 189 M 0.6767 0.0214 0.3018 190 G 0.2014 0.0244 0.7742 191 A 0.0101 0.8025 0.1874 192 E 0.0064 0.8954 0.0982 193 G 0.0065 0.9333 0.0602 194 A 0.0092 0.9375 0.0533 195 A 0.0169 0.9200 0.0632 196 N 0.0274 0.8835 0.0891 197 V 0.0302 0.8337 0.1362 198 I 0.0622 0.6936 0.2443 199 F 0.0581 0.4942 0.4478 200 R 0.0413 0.4243 0.5344 201 K 0.0434 0.4134 0.5433 202 E 0.0172 0.6026 0.3802 203 I 0.0216 0.6014 0.3770 204 K 0.0187 0.5817 0.3996 205 A 0.0184 0.5626 0.4190 206 A 0.0162 0.6345 0.3492 207 D 0.0116 0.7031 0.2852 208 D 0.0154 0.7345 0.2500 209 P 0.0076 0.8005 0.1919 210 D 0.0111 0.8356 0.1533 211 A 0.0062 0.8606 0.1332 212 M 0.0087 0.8579 0.1335 213 R 0.0095 0.8479 0.1426 214 A 0.0093 0.8483 0.1424 215 E 0.0125 0.8370 0.1506 216 K 0.0098 0.8226 0.1677 217 I 0.0140 0.8527 0.1333 218 E 0.0172 0.8268 0.1559 219 E 0.0232 0.7713 0.2055 220 Y 0.0223 0.7361 0.2416 221 Q 0.0149 0.7550 0.2302 222 N 0.0136 0.6810 0.3054 223 A 0.0241 0.5283 0.4475 224 F 0.0419 0.2326 0.7256 225 N 0.0700 0.1271 0.8029 226 T 0.0695 0.0806 0.8499 227 P 0.0070 0.8999 0.0931 228 Y 0.0052 0.9300 0.0648 229 V 0.0057 0.9430 0.0513 230 A 0.0066 0.9444 0.0490 231 A 0.0063 0.9376 0.0561 232 A 0.0059 0.8930 0.1011 233 R 0.0430 0.4472 0.5099 234 G 0.0353 0.0764 0.8883 235 Q 0.0852 0.1224 0.7924 236 V 0.2316 0.1482 0.6202 237 D 0.2403 0.2208 0.5389 238 D 0.3217 0.1875 0.4908 239 V 0.4518 0.0777 0.4705 240 I 0.3998 0.0324 0.5677 241 D 0.1441 0.0272 0.8287 242 P 0.0108 0.7136 0.2756 243 A 0.0073 0.8240 0.1686 244 D 0.0086 0.8681 0.1233 245 T 0.0074 0.8843 0.1083 246 R 0.0044 0.9371 0.0585 247 R 0.0044 0.9525 0.0431 248 K 0.0044 0.9586 0.0370 249 I 0.0044 0.9588 0.0368 250 A 0.0044 0.9598 0.0358 251 S 0.0044 0.9583 0.0374 252 A 0.0044 0.9557 0.0399 253 L 0.0044 0.9530 0.0426 254 E 0.0045 0.9393 0.0562 255 M 0.0050 0.9094 0.0856 256 Y 0.0072 0.8515 0.1414 257 A 0.0126 0.6663 0.3210 258 T 0.0278 0.3259 0.6463 259 K 0.0519 0.2154 0.7327 260 R 0.0740 0.2391 0.6869 261 Q 0.0956 0.2399 0.6645 262 T 0.0962 0.1719 0.7319 263 R 0.0714 0.0974 0.8312 264 P 0.0670 0.1210 0.8119 265 A 0.0753 0.2112 0.7135 266 K 0.0873 0.2284 0.6843 267 K 0.0906 0.2125 0.6969 268 H 0.1026 0.1599 0.7375 269 G 0.0894 0.1010 0.8096 270 N 0.1264 0.1033 0.7703 271 F 0.1891 0.0591 0.7518 272 P 0.1168 0.0398 0.8434 273 C 0.0439 0.0348 0.9214