# This file is the result of combining several RDB files, specifically # T0219.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0219.t2k.stride-ebghtl.rdb (weight 1.24869) # T0219.t2k.str2.rdb (weight 1.54758) # T0219.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 T0219.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0219 # 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 T0219.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 92 # # ============================================ # Comments from T0219.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0219 # 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 T0219.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 92 # # ============================================ # Comments from T0219.t2k.str2.rdb # ============================================ # TARGET T0219 # 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 T0219.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 92 # # ============================================ # Comments from T0219.t2k.alpha.rdb # ============================================ # TARGET T0219 # 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 T0219.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 92 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0945 0.0514 0.8541 2 S 0.2217 0.0861 0.6921 3 A 0.2393 0.1142 0.6465 4 V 0.1674 0.1086 0.7240 5 T 0.0667 0.4262 0.5071 6 E 0.0344 0.5218 0.4438 7 S 0.0511 0.5539 0.3950 8 V 0.0851 0.5792 0.3357 9 L 0.0674 0.6580 0.2746 10 E 0.0727 0.7259 0.2014 11 S 0.0672 0.7467 0.1862 12 I 0.0736 0.6961 0.2303 13 I 0.0665 0.5919 0.3416 14 S 0.0541 0.3310 0.6149 15 P 0.0710 0.1776 0.7514 16 V 0.1975 0.0275 0.7750 17 T 0.1340 0.0207 0.8453 18 M 0.0061 0.9203 0.0736 19 S 0.0048 0.9419 0.0532 20 E 0.0049 0.9464 0.0487 21 F 0.0053 0.9355 0.0592 22 L 0.0064 0.9041 0.0895 23 E 0.0081 0.8235 0.1684 24 E 0.0158 0.7054 0.2788 25 Y 0.0479 0.4655 0.4865 26 W 0.0602 0.2292 0.7105 27 P 0.0548 0.1702 0.7750 28 V 0.0831 0.1225 0.7944 29 K 0.1498 0.0306 0.8196 30 P 0.3370 0.0145 0.6485 31 L 0.7923 0.0133 0.1944 32 V 0.8655 0.0133 0.1212 33 A 0.8209 0.0170 0.1621 34 R 0.5329 0.0541 0.4130 35 G 0.1792 0.0537 0.7671 36 E 0.1040 0.0715 0.8245 37 V 0.0803 0.0960 0.8237 38 E 0.0230 0.2422 0.7348 39 R 0.0290 0.1809 0.7901 40 F 0.0745 0.2141 0.7114 41 T 0.0883 0.1700 0.7417 42 S 0.0755 0.1477 0.7768 43 I 0.0651 0.1961 0.7388 44 P 0.1122 0.0935 0.7943 45 G 0.0989 0.0592 0.8419 46 F 0.0070 0.8782 0.1148 47 E 0.0054 0.9030 0.0916 48 K 0.0053 0.9310 0.0637 49 V 0.0053 0.9281 0.0666 50 R 0.0061 0.9077 0.0863 51 T 0.0074 0.8427 0.1499 52 L 0.0101 0.7868 0.2031 53 E 0.0301 0.6682 0.3017 54 N 0.0310 0.4556 0.5134 55 V 0.0418 0.4249 0.5334 56 L 0.0591 0.3780 0.5630 57 A 0.0859 0.2630 0.6511 58 I 0.1375 0.2027 0.6598 59 Y 0.1803 0.1988 0.6209 60 N 0.2243 0.1897 0.5860 61 N 0.3058 0.1824 0.5118 62 P 0.4706 0.1519 0.3775 63 V 0.6178 0.1041 0.2780 64 M 0.7200 0.0825 0.1975 65 V 0.7335 0.0747 0.1917 66 V 0.5429 0.0873 0.3698 67 G 0.2885 0.1117 0.5998 68 D 0.0952 0.0677 0.8371 69 A 0.1272 0.0551 0.8177 70 V 0.3870 0.0395 0.5735 71 I 0.6320 0.0375 0.3305 72 E 0.5898 0.0615 0.3487 73 E 0.4953 0.0939 0.4108 74 S 0.2948 0.1378 0.5675 75 E 0.1639 0.1117 0.7243 76 G 0.1159 0.1024 0.7816 77 I 0.1187 0.2139 0.6674 78 T 0.1119 0.3003 0.5878 79 D 0.1152 0.3915 0.4934 80 R 0.0912 0.5348 0.3740 81 F 0.0913 0.5579 0.3509 82 L 0.1084 0.5184 0.3732 83 V 0.0995 0.4598 0.4407 84 S 0.1044 0.3012 0.5944 85 P 0.0400 0.5668 0.3932 86 A 0.0367 0.5813 0.3821 87 E 0.0415 0.5905 0.3680 88 A 0.0510 0.5463 0.4028 89 L 0.0387 0.5239 0.4374 90 E 0.0448 0.4211 0.5341 91 W 0.0664 0.3085 0.6251 92 Y 0.0629 0.2711 0.6660 93 E 0.0599 0.2662 0.6738 94 K 0.0737 0.1887 0.7376 95 G 0.1131 0.1167 0.7702 96 A 0.3590 0.0593 0.5817 97 A 0.6963 0.0383 0.2654 98 L 0.8191 0.0306 0.1504 99 E 0.7881 0.0410 0.1708 100 F 0.6719 0.0577 0.2703 101 D 0.3376 0.1094 0.5530 102 F 0.2034 0.0890 0.7076 103 T 0.0906 0.3198 0.5897 104 D 0.0687 0.3764 0.5550 105 L 0.0463 0.4202 0.5336 106 F 0.0624 0.3004 0.6372 107 I 0.0527 0.2730 0.6744 108 P 0.0141 0.6739 0.3120 109 Q 0.0133 0.7415 0.2452 110 V 0.0091 0.8528 0.1380 111 R 0.0071 0.8935 0.0994 112 R 0.0075 0.8919 0.1006 113 W 0.0073 0.8967 0.0960 114 I 0.0098 0.8692 0.1210 115 E 0.0100 0.8116 0.1783 116 K 0.0145 0.7293 0.2562 117 L 0.0630 0.5324 0.4046 118 K 0.0664 0.4140 0.5196 119 A 0.0655 0.4312 0.5033 120 E 0.0612 0.4016 0.5372 121 L 0.0589 0.3211 0.6200 122 R 0.0607 0.2143 0.7250 123 L 0.0870 0.1546 0.7584 124 P 0.0812 0.2394 0.6794 125 A 0.0766 0.2874 0.6361 126 G 0.1109 0.2196 0.6694 127 T 0.1797 0.1426 0.6777 128 S 0.2241 0.1065 0.6695 129 S 0.2813 0.1092 0.6095 130 K 0.5488 0.0662 0.3850 131 A 0.7840 0.0253 0.1907 132 I 0.8695 0.0194 0.1110 133 V 0.8902 0.0109 0.0989 134 Y 0.8639 0.0124 0.1237 135 A 0.7446 0.0169 0.2385 136 A 0.4296 0.0218 0.5486 137 K 0.1562 0.0675 0.7763 138 N 0.0591 0.1098 0.8311 139 G 0.0636 0.0955 0.8409 140 G 0.0995 0.0645 0.8360 141 G 0.1795 0.0493 0.7712 142 F 0.3037 0.0432 0.6531 143 K 0.2930 0.0547 0.6522 144 A 0.4458 0.0826 0.4716 145 H 0.4485 0.0797 0.4718 146 F 0.4603 0.0413 0.4984 147 D 0.2475 0.0190 0.7336 148 A 0.0464 0.1740 0.7796 149 Y 0.0596 0.1614 0.7789 150 T 0.0717 0.1570 0.7713 151 N 0.4119 0.0757 0.5124 152 L 0.8312 0.0234 0.1453 153 I 0.9125 0.0096 0.0780 154 F 0.9163 0.0085 0.0752 155 Q 0.9080 0.0088 0.0831 156 I 0.8666 0.0135 0.1199 157 Q 0.5887 0.0345 0.3768 158 G 0.4125 0.0281 0.5594 159 E 0.5960 0.0218 0.3822 160 K 0.7677 0.0094 0.2229 161 T 0.8557 0.0072 0.1371 162 W 0.8887 0.0049 0.1064 163 K 0.8975 0.0048 0.0977 164 L 0.8524 0.0091 0.1385 165 A 0.5958 0.0113 0.3929 166 K 0.2260 0.0176 0.7564 167 N 0.1003 0.1137 0.7860 168 E 0.0671 0.1797 0.7533 169 N 0.0831 0.1758 0.7411 170 V 0.0758 0.2108 0.7134 171 S 0.0668 0.2594 0.6738 172 N 0.1231 0.1957 0.6812 173 P 0.1516 0.1779 0.6704 174 M 0.1698 0.1225 0.7076 175 Q 0.1603 0.1267 0.7130 176 H 0.1325 0.1220 0.7455 177 Y 0.1088 0.2321 0.6591 178 D 0.1257 0.2547 0.6196 179 L 0.1216 0.3173 0.5610 180 S 0.1069 0.3137 0.5794 181 E 0.1274 0.2513 0.6214 182 A 0.1485 0.1800 0.6715 183 P 0.1516 0.1474 0.7010 184 Y 0.1435 0.1663 0.6902 185 Y 0.1111 0.1611 0.7277 186 P 0.0964 0.1811 0.7225 187 D 0.1097 0.2582 0.6321 188 D 0.1343 0.2713 0.5944 189 L 0.1454 0.2626 0.5920 190 Q 0.1425 0.2318 0.6257 191 S 0.1587 0.2017 0.6396 192 Y 0.1398 0.2199 0.6403 193 W 0.1284 0.1549 0.7166 194 K 0.0778 0.3215 0.6006 195 G 0.0613 0.3166 0.6221 196 D 0.0705 0.2451 0.6844 197 P 0.0807 0.2234 0.6959 198 P 0.0982 0.2404 0.6613 199 K 0.0891 0.2384 0.6725 200 E 0.0761 0.2116 0.7123 201 D 0.0659 0.1516 0.7825 202 L 0.0800 0.0840 0.8359 203 P 0.0945 0.0615 0.8440 204 D 0.1733 0.0562 0.7705 205 A 0.3669 0.0577 0.5754 206 E 0.6152 0.0428 0.3420 207 I 0.8043 0.0251 0.1706 208 V 0.8686 0.0107 0.1207 209 N 0.8718 0.0082 0.1200 210 L 0.7706 0.0087 0.2206 211 T 0.2858 0.0140 0.7002 212 P 0.0447 0.0856 0.8698 213 G 0.0428 0.0587 0.8986 214 T 0.3463 0.0374 0.6163 215 M 0.7859 0.0095 0.2046 216 L 0.8843 0.0073 0.1084 217 Y 0.8855 0.0068 0.1078 218 L 0.7749 0.0078 0.2173 219 P 0.3038 0.0133 0.6828 220 R 0.0495 0.1112 0.8393 221 G 0.0768 0.0901 0.8331 222 L 0.2832 0.0964 0.6204 223 W 0.4961 0.0497 0.4542 224 H 0.6769 0.0467 0.2763 225 S 0.7667 0.0264 0.2069 226 T 0.8053 0.0201 0.1746 227 K 0.7716 0.0214 0.2070 228 S 0.6220 0.0242 0.3538 229 D 0.2416 0.1200 0.6384 230 Q 0.1488 0.0855 0.7657 231 A 0.1996 0.1155 0.6848 232 T 0.4725 0.0334 0.4940 233 L 0.7746 0.0160 0.2094 234 A 0.8764 0.0074 0.1162 235 L 0.8860 0.0076 0.1064 236 N 0.8978 0.0053 0.0970 237 I 0.8590 0.0110 0.1299 238 T 0.8291 0.0122 0.1586 239 F 0.7536 0.0211 0.2253 240 G 0.5780 0.0292 0.3927 241 Q 0.3222 0.0334 0.6444 242 P 0.1160 0.1121 0.7719 243 A 0.0883 0.1838 0.7279 244 W 0.0206 0.7072 0.2722 245 L 0.0091 0.8505 0.1404 246 D 0.0086 0.8737 0.1177 247 L 0.0080 0.8856 0.1064 248 M 0.0071 0.8908 0.1020 249 L 0.0063 0.8897 0.1040 250 A 0.0073 0.8650 0.1277 251 A 0.0134 0.8027 0.1839 252 L 0.0349 0.7024 0.2628 253 R 0.0157 0.6317 0.3526 254 K 0.0261 0.5878 0.3861 255 K 0.0747 0.4900 0.4353 256 L 0.0901 0.3949 0.5150 257 I 0.0917 0.3237 0.5845 258 S 0.0658 0.2868 0.6474 259 D 0.0477 0.3830 0.5693 260 N 0.0567 0.3861 0.5573 261 R 0.0748 0.4551 0.4701 262 F 0.1067 0.4321 0.4611 263 R 0.1042 0.4255 0.4702 264 E 0.0901 0.2926 0.6173 265 L 0.0398 0.2653 0.6949 266 A 0.0395 0.1412 0.8193 267 V 0.0762 0.0585 0.8654 268 N 0.0895 0.0653 0.8452 269 H 0.0505 0.3874 0.5621 270 Q 0.0308 0.3900 0.5793 271 S 0.0413 0.3609 0.5979 272 L 0.0617 0.1449 0.7934 273 H 0.0233 0.4386 0.5381 274 E 0.0097 0.6349 0.3554 275 S 0.0169 0.6484 0.3347 276 S 0.0266 0.5814 0.3920 277 K 0.0222 0.6370 0.3408 278 S 0.0070 0.8655 0.1275 279 E 0.0064 0.8931 0.1005 280 L 0.0061 0.9154 0.0784 281 N 0.0055 0.9343 0.0602 282 G 0.0053 0.9369 0.0578 283 Y 0.0052 0.9390 0.0558 284 L 0.0049 0.9480 0.0472 285 E 0.0048 0.9513 0.0439 286 S 0.0049 0.9464 0.0487 287 L 0.0049 0.9467 0.0484 288 I 0.0051 0.9396 0.0553 289 Q 0.0058 0.9096 0.0846 290 T 0.0072 0.8715 0.1213 291 L 0.0080 0.8664 0.1257 292 S 0.0064 0.8816 0.1120 293 E 0.0071 0.8483 0.1446 294 N 0.0108 0.7825 0.2067 295 A 0.0105 0.8088 0.1807 296 E 0.0087 0.7682 0.2231 297 T 0.0110 0.7600 0.2290 298 L 0.0235 0.7073 0.2692 299 T 0.0346 0.6699 0.2955 300 P 0.0080 0.8575 0.1345 301 E 0.0072 0.8861 0.1067 302 Q 0.0081 0.8875 0.1044 303 I 0.0117 0.8478 0.1405 304 F 0.0184 0.7506 0.2310 305 Q 0.0205 0.6137 0.3658 306 S 0.0323 0.4830 0.4847 307 Q 0.0401 0.4068 0.5531 308 D 0.0385 0.3941 0.5675 309 S 0.0307 0.4654 0.5038 310 D 0.0334 0.4749 0.4917 311 F 0.0536 0.4029 0.5435 312 D 0.0600 0.4085 0.5315 313 P 0.0626 0.3521 0.5853 314 Y 0.0554 0.3880 0.5566 315 Q 0.0447 0.4051 0.5501 316 S 0.0625 0.3332 0.6043 317 T 0.0602 0.3114 0.6283 318 Q 0.0501 0.3737 0.5761 319 L 0.1050 0.3804 0.5146 320 V 0.1025 0.3782 0.5194 321 F 0.0362 0.7048 0.2590 322 R 0.0223 0.7526 0.2252 323 Q 0.0369 0.7715 0.1916 324 L 0.0352 0.8422 0.1226 325 L 0.0359 0.8433 0.1208 326 T 0.0418 0.8184 0.1398 327 S 0.0517 0.7621 0.1862 328 Y 0.1321 0.5134 0.3545 329 K 0.1314 0.2944 0.5742 330 F 0.0585 0.0339 0.9076