# This file is the result of combining several RDB files, specifically # T0133.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0133.t2k.stride-ebghtl.rdb (weight 1.24869) # T0133.t2k.str.rdb (weight 1.53983) # T0133.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 T0133.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0133 # 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 T0133.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 13 # # ============================================ # Comments from T0133.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0133 # 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 T0133.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 13 # # ============================================ # Comments from T0133.t2k.str.rdb # ============================================ # TARGET T0133 # 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 T0133.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 13 # # ============================================ # Comments from T0133.t2k.alpha.rdb # ============================================ # TARGET T0133 # 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 T0133.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 13 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0562 0.0535 0.8903 2 N 0.0979 0.1118 0.7903 3 S 0.1090 0.1875 0.7035 4 I 0.0917 0.3419 0.5663 5 K 0.0853 0.3178 0.5969 6 N 0.1233 0.2733 0.6033 7 V 0.1623 0.1598 0.6779 8 P 0.1716 0.2215 0.6069 9 A 0.2318 0.3896 0.3786 10 R 0.3074 0.4046 0.2880 11 V 0.3231 0.4252 0.2518 12 L 0.3090 0.3374 0.3536 13 S 0.2769 0.2018 0.5213 14 R 0.2153 0.1335 0.6512 15 R 0.1157 0.0465 0.8378 16 P 0.0427 0.1056 0.8517 17 G 0.0389 0.0819 0.8791 18 H 0.1174 0.1140 0.7686 19 S 0.1643 0.2330 0.6027 20 L 0.1024 0.4905 0.4071 21 E 0.0901 0.6207 0.2892 22 A 0.0477 0.6823 0.2700 23 E 0.0487 0.6854 0.2659 24 R 0.0202 0.7888 0.1910 25 E 0.0159 0.8087 0.1754 26 Q 0.0132 0.7998 0.1870 27 F 0.0131 0.8014 0.1855 28 D 0.0100 0.8452 0.1448 29 K 0.0057 0.9074 0.0869 30 T 0.0063 0.8947 0.0990 31 Q 0.0047 0.9246 0.0707 32 A 0.0045 0.9394 0.0560 33 I 0.0051 0.9439 0.0510 34 S 0.0050 0.9386 0.0564 35 I 0.0061 0.9318 0.0620 36 S 0.0066 0.9128 0.0806 37 K 0.0086 0.8294 0.1620 38 A 0.0154 0.7457 0.2389 39 I 0.0571 0.4448 0.4981 40 N 0.0707 0.1612 0.7681 41 S 0.0679 0.3884 0.5436 42 Q 0.0667 0.4211 0.5122 43 E 0.0693 0.3917 0.5390 44 A 0.0829 0.1077 0.8094 45 P 0.0641 0.0667 0.8692 46 V 0.0794 0.0777 0.8429 47 K 0.0850 0.1809 0.7341 48 E 0.0626 0.5355 0.4019 49 K 0.0642 0.4838 0.4520 50 H 0.1468 0.4274 0.4258 51 A 0.2051 0.4881 0.3068 52 R 0.2127 0.5479 0.2395 53 R 0.3344 0.4990 0.1666 54 I 0.4842 0.4011 0.1147 55 I 0.5461 0.3186 0.1353 56 L 0.5404 0.2434 0.2162 57 G 0.5023 0.1624 0.3353 58 T 0.3416 0.1099 0.5485 59 H 0.1431 0.2191 0.6378 60 H 0.0599 0.3048 0.6353 61 E 0.0366 0.5592 0.4043 62 K 0.0240 0.6580 0.3180 63 G 0.0271 0.7087 0.2642 64 A 0.0354 0.8110 0.1536 65 F 0.0389 0.8682 0.0929 66 T 0.0497 0.8808 0.0695 67 F 0.0520 0.8837 0.0643 68 W 0.0607 0.8721 0.0672 69 S 0.0549 0.8611 0.0840 70 Y 0.0390 0.8488 0.1122 71 A 0.0774 0.7218 0.2009 72 I 0.0954 0.5638 0.3408 73 G 0.1252 0.3903 0.4844 74 L 0.1713 0.1589 0.6698 75 P 0.1420 0.0995 0.7585 76 L 0.0745 0.1671 0.7585 77 P 0.0374 0.1995 0.7631 78 S 0.0323 0.1726 0.7951 79 S 0.0677 0.1755 0.7568 80 S 0.0508 0.4944 0.4548 81 I 0.0947 0.7301 0.1751 82 L 0.0557 0.8640 0.0802 83 S 0.0143 0.9373 0.0484 84 W 0.0066 0.9525 0.0409 85 K 0.0047 0.9572 0.0381 86 F 0.0047 0.9589 0.0364 87 C 0.0044 0.9597 0.0359 88 H 0.0048 0.9588 0.0364 89 V 0.0046 0.9580 0.0374 90 L 0.0046 0.9561 0.0392 91 H 0.0049 0.9558 0.0394 92 K 0.0054 0.9515 0.0430 93 V 0.0080 0.9407 0.0514 94 L 0.0134 0.9177 0.0689 95 R 0.0331 0.8329 0.1340 96 D 0.0252 0.6193 0.3555 97 G 0.0330 0.2243 0.7427 98 H 0.0768 0.0627 0.8605 99 P 0.0170 0.5053 0.4777 100 N 0.0192 0.5099 0.4710 101 V 0.0454 0.6490 0.3057 102 L 0.0456 0.7118 0.2426 103 H 0.0161 0.8321 0.1518 104 D 0.0154 0.8292 0.1554 105 C 0.0191 0.7886 0.1923 106 Q 0.0267 0.7493 0.2240 107 R 0.0301 0.6581 0.3118 108 Y 0.0459 0.5859 0.3683 109 R 0.0298 0.7151 0.2551 110 S 0.0280 0.6840 0.2880 111 N 0.0485 0.7597 0.1918 112 I 0.0976 0.7801 0.1223 113 R 0.1165 0.7663 0.1171 114 E 0.1313 0.7257 0.1431 115 I 0.0753 0.7982 0.1265 116 G 0.0678 0.7795 0.1527 117 D 0.0563 0.7270 0.2167 118 L 0.0818 0.5970 0.3213 119 W 0.0882 0.3988 0.5130 120 G 0.0506 0.2444 0.7051 121 H 0.0551 0.1888 0.7561 122 L 0.0524 0.1794 0.7682 123 R 0.0488 0.2229 0.7283 124 D 0.0383 0.2969 0.6647 125 Q 0.0364 0.3022 0.6614 126 Y 0.0389 0.4913 0.4699 127 G 0.0228 0.6720 0.3051 128 H 0.0137 0.8470 0.1393 129 L 0.0091 0.9122 0.0787 130 V 0.0061 0.9460 0.0479 131 N 0.0052 0.9538 0.0409 132 I 0.0048 0.9561 0.0391 133 Y 0.0044 0.9568 0.0388 134 T 0.0044 0.9576 0.0380 135 K 0.0046 0.9536 0.0419 136 L 0.0046 0.9458 0.0495 137 L 0.0046 0.9450 0.0505 138 L 0.0047 0.9402 0.0551 139 T 0.0052 0.9212 0.0736 140 K 0.0082 0.8793 0.1125 141 I 0.0313 0.8258 0.1429 142 S 0.0389 0.7903 0.1708 143 F 0.0441 0.7272 0.2287 144 H 0.0658 0.6049 0.3293 145 L 0.0609 0.4205 0.5186 146 K 0.0727 0.3229 0.6044 147 H 0.0921 0.0859 0.8220 148 P 0.0506 0.1423 0.8072 149 Q 0.1019 0.1457 0.7524 150 F 0.1076 0.0928 0.7996 151 P 0.0762 0.1254 0.7984 152 A 0.0659 0.1287 0.8054 153 G 0.0986 0.1494 0.7520 154 L 0.1536 0.1375 0.7089 155 E 0.2539 0.1112 0.6349 156 V 0.2384 0.1712 0.5904 157 T 0.1664 0.1620 0.6716 158 D 0.0681 0.6636 0.2683 159 E 0.0665 0.7014 0.2321 160 V 0.1053 0.6606 0.2341 161 L 0.1104 0.6098 0.2798 162 E 0.1157 0.5713 0.3130 163 K 0.0897 0.6080 0.3023 164 A 0.0949 0.5032 0.4018 165 A 0.1354 0.3022 0.5625 166 G 0.1136 0.1837 0.7027 167 T 0.1327 0.1330 0.7342 168 D 0.1189 0.0576 0.8235 169 V 0.0232 0.2328 0.7440 170 N 0.0272 0.1977 0.7751 171 N 0.0730 0.2296 0.6974 172 I 0.1842 0.2815 0.5343 173 F 0.4577 0.2387 0.3036 174 Q 0.6210 0.1928 0.1862 175 L 0.5753 0.2398 0.1849 176 T 0.6340 0.2004 0.1656 177 V 0.5393 0.2507 0.2099 178 E 0.4185 0.2303 0.3512 179 M 0.0762 0.7299 0.1939 180 F 0.0230 0.8129 0.1641 181 D 0.0167 0.8154 0.1679 182 Y 0.0118 0.8301 0.1581 183 M 0.0097 0.8280 0.1623 184 D 0.0090 0.7666 0.2244 185 C 0.0129 0.6942 0.2928 186 E 0.0110 0.8553 0.1338 187 L 0.0056 0.9026 0.0918 188 K 0.0053 0.9221 0.0726 189 L 0.0046 0.9433 0.0521 190 S 0.0045 0.9499 0.0456 191 E 0.0046 0.9527 0.0427 192 S 0.0046 0.9509 0.0445 193 V 0.0051 0.9515 0.0434 194 F 0.0052 0.9424 0.0524 195 R 0.0057 0.9245 0.0698 196 Q 0.0063 0.8939 0.0998 197 L 0.0265 0.7683 0.2052 198 N 0.0317 0.5089 0.4594 199 T 0.0489 0.3559 0.5952 200 A 0.0872 0.2589 0.6538 201 I 0.1117 0.2077 0.6806 202 A 0.1190 0.2262 0.6548 203 V 0.1335 0.2310 0.6355 204 S 0.1478 0.2156 0.6366 205 Q 0.1807 0.1975 0.6218 206 M 0.1514 0.1144 0.7343 207 S 0.0847 0.1691 0.7462 208 S 0.0409 0.1665 0.7926 209 G 0.0476 0.1393 0.8131 210 Q 0.2784 0.2072 0.5144 211 C 0.6237 0.1281 0.2482 212 R 0.5563 0.1681 0.2756 213 L 0.3911 0.3545 0.2544 214 A 0.1425 0.6003 0.2572 215 P 0.0803 0.7125 0.2072 216 L 0.0183 0.8769 0.1049 217 I 0.0095 0.9295 0.0610 218 Q 0.0060 0.9437 0.0502 219 V 0.0046 0.9485 0.0469 220 I 0.0047 0.9482 0.0471 221 Q 0.0051 0.9318 0.0631 222 D 0.0068 0.8757 0.1174 223 C 0.0095 0.8242 0.1664 224 S 0.0214 0.7962 0.1824 225 H 0.0066 0.8281 0.1653 226 L 0.0049 0.9161 0.0790 227 Y 0.0044 0.9486 0.0470 228 H 0.0044 0.9573 0.0383 229 Y 0.0044 0.9597 0.0359 230 T 0.0044 0.9600 0.0356 231 V 0.0044 0.9594 0.0362 232 K 0.0045 0.9580 0.0375 233 L 0.0045 0.9553 0.0402 234 M 0.0046 0.9487 0.0467 235 F 0.0050 0.9331 0.0619 236 K 0.0056 0.8716 0.1228 237 L 0.0111 0.7777 0.2111 238 H 0.0244 0.6328 0.3428 239 S 0.0210 0.4628 0.5162 240 C 0.0336 0.3076 0.6588 241 L 0.0608 0.1194 0.8198 242 P 0.0595 0.0867 0.8539 243 A 0.0087 0.7444 0.2469 244 D 0.0069 0.7883 0.2048 245 T 0.0082 0.8483 0.1435 246 L 0.0119 0.8361 0.1520 247 Q 0.0098 0.8517 0.1385 248 G 0.0071 0.8640 0.1289 249 H 0.0097 0.8670 0.1233 250 R 0.0065 0.9067 0.0868 251 D 0.0068 0.8860 0.1071 252 R 0.0056 0.8998 0.0946 253 F 0.0052 0.9134 0.0814 254 H 0.0048 0.9239 0.0713 255 E 0.0050 0.9218 0.0733 256 Q 0.0049 0.9288 0.0663 257 F 0.0052 0.9351 0.0597 258 H 0.0050 0.9242 0.0707 259 S 0.0052 0.9161 0.0787 260 L 0.0047 0.9370 0.0583 261 R 0.0046 0.9465 0.0488 262 N 0.0048 0.9389 0.0563 263 F 0.0049 0.9288 0.0663 264 F 0.0053 0.9128 0.0819 265 R 0.0054 0.8300 0.1645 266 R 0.0086 0.6886 0.3028 267 A 0.0228 0.6667 0.3106 268 S 0.0140 0.5686 0.4174 269 D 0.0145 0.5806 0.4049 270 M 0.0468 0.7269 0.2263 271 L 0.0436 0.7813 0.1751 272 Y 0.0817 0.7510 0.1673 273 F 0.1109 0.7205 0.1685 274 K 0.0861 0.7107 0.2031 275 R 0.1108 0.6219 0.2673 276 L 0.1992 0.4701 0.3307 277 I 0.3149 0.2334 0.4517 278 Q 0.3100 0.1403 0.5497 279 I 0.2284 0.0579 0.7137 280 P 0.1310 0.0583 0.8107 281 R 0.1506 0.0562 0.7932 282 L 0.1201 0.0347 0.8452 283 P 0.0815 0.0503 0.8682 284 E 0.0729 0.0868 0.8403 285 G 0.0673 0.0597 0.8730 286 P 0.0666 0.0609 0.8725 287 P 0.0621 0.1402 0.7977 288 N 0.0877 0.1843 0.7280 289 F 0.1108 0.2735 0.6157 290 L 0.1714 0.2405 0.5881 291 R 0.1572 0.2201 0.6227 292 A 0.0494 0.5712 0.3794 293 S 0.0267 0.5370 0.4363 294 A 0.0320 0.5080 0.4599 295 L 0.0244 0.6425 0.3331 296 A 0.0143 0.7149 0.2708 297 E 0.0157 0.6492 0.3351 298 H 0.0393 0.4902 0.4705 299 I 0.0897 0.2241 0.6861 300 K 0.0837 0.1086 0.8077 301 P 0.0964 0.0882 0.8154 302 V 0.1224 0.0539 0.8237 303 V 0.1548 0.0465 0.7986 304 V 0.3224 0.0664 0.6112 305 I 0.3098 0.0636 0.6266 306 P 0.1754 0.0690 0.7555 307 E 0.1224 0.1230 0.7546 308 E 0.0961 0.0778 0.8261 309 A 0.0735 0.0697 0.8567 310 P 0.0669 0.0777 0.8554 311 E 0.0566 0.0678 0.8756 312 E 0.0384 0.0411 0.9205