# This file is the result of combining several RDB files, specifically # T0293.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0293.t2k.stride-ebghtl.rdb (weight 1.24869) # T0293.t2k.str2.rdb (weight 1.54758) # T0293.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 T0293.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 417 # # ============================================ # Comments from T0293.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 417 # # ============================================ # Comments from T0293.t2k.str2.rdb # ============================================ # TARGET T0293 # 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 T0293.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 417 # # ============================================ # Comments from T0293.t2k.alpha.rdb # ============================================ # TARGET T0293 # 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 T0293.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 417 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.1193 0.0558 0.8250 2 I 0.2242 0.0328 0.7430 3 P 0.1079 0.0272 0.8649 4 L 0.0356 0.1845 0.7799 5 E 0.0389 0.1512 0.8100 6 R 0.2599 0.1121 0.6280 7 L 0.5137 0.0311 0.4552 8 I 0.4739 0.0190 0.5071 9 P 0.2831 0.0252 0.6917 10 T 0.1118 0.0368 0.8514 11 V 0.0636 0.1414 0.7950 12 P 0.0366 0.3489 0.6145 13 L 0.0313 0.4998 0.4689 14 R 0.0179 0.7933 0.1888 15 L 0.0131 0.8758 0.1111 16 N 0.0120 0.9026 0.0853 17 Y 0.0085 0.9380 0.0535 18 I 0.0078 0.9485 0.0437 19 H 0.0083 0.9460 0.0457 20 W 0.0092 0.9428 0.0479 21 V 0.0078 0.9404 0.0519 22 E 0.0059 0.9408 0.0533 23 D 0.0054 0.9340 0.0606 24 L 0.0069 0.9075 0.0857 25 I 0.0102 0.8420 0.1478 26 G 0.0140 0.6862 0.2998 27 H 0.0241 0.4624 0.5134 28 Q 0.0429 0.3645 0.5926 29 D 0.0709 0.3182 0.6109 30 S 0.0749 0.3085 0.6166 31 D 0.0716 0.2868 0.6416 32 K 0.0621 0.2680 0.6699 33 S 0.0588 0.1689 0.7723 34 T 0.0808 0.1382 0.7811 35 L 0.1683 0.0705 0.7612 36 R 0.3690 0.0353 0.5957 37 R 0.7440 0.0164 0.2396 38 G 0.8862 0.0134 0.1004 39 I 0.8780 0.0147 0.1073 40 D 0.8658 0.0126 0.1216 41 I 0.5926 0.0610 0.3463 42 G 0.2110 0.0797 0.7093 43 T 0.0825 0.1906 0.7270 44 G 0.0509 0.3572 0.5919 45 A 0.0235 0.6357 0.3408 46 S 0.0169 0.7034 0.2796 47 C 0.0069 0.9358 0.0573 48 I 0.0048 0.9524 0.0428 49 Y 0.0051 0.9547 0.0402 50 P 0.0060 0.9527 0.0413 51 L 0.0061 0.9471 0.0468 52 L 0.0100 0.9277 0.0623 53 G 0.0113 0.8851 0.1036 54 A 0.0215 0.7870 0.1915 55 T 0.0388 0.5984 0.3628 56 L 0.0761 0.1808 0.7431 57 N 0.0239 0.1295 0.8465 58 G 0.0277 0.0764 0.8959 59 W 0.2773 0.0281 0.6946 60 Y 0.7643 0.0076 0.2281 61 F 0.9104 0.0032 0.0864 62 L 0.8886 0.0114 0.1000 63 A 0.8926 0.0064 0.1010 64 T 0.8227 0.0123 0.1650 65 E 0.6242 0.0157 0.3601 66 V 0.1730 0.0398 0.7871 67 D 0.0757 0.0268 0.8974 68 D 0.0051 0.9092 0.0856 69 M 0.0049 0.9439 0.0513 70 C 0.0048 0.9539 0.0413 71 F 0.0047 0.9603 0.0351 72 N 0.0047 0.9598 0.0355 73 Y 0.0047 0.9593 0.0361 74 A 0.0047 0.9596 0.0357 75 K 0.0047 0.9599 0.0354 76 K 0.0047 0.9590 0.0363 77 N 0.0047 0.9577 0.0375 78 V 0.0049 0.9507 0.0444 79 E 0.0052 0.9350 0.0598 80 Q 0.0102 0.8240 0.1658 81 N 0.0480 0.4317 0.5203 82 N 0.0584 0.1207 0.8209 83 L 0.0468 0.2700 0.6832 84 S 0.0394 0.3980 0.5626 85 D 0.0673 0.3918 0.5409 86 L 0.2492 0.2566 0.4942 87 I 0.6201 0.1246 0.2553 88 K 0.7620 0.0958 0.1422 89 V 0.7797 0.0974 0.1228 90 V 0.6883 0.1262 0.1856 91 K 0.5285 0.1520 0.3195 92 V 0.2365 0.2110 0.5525 93 P 0.1395 0.2173 0.6432 94 Q 0.0693 0.4588 0.4719 95 A 0.0598 0.4376 0.5025 96 T 0.0647 0.4385 0.4968 97 L 0.0626 0.5064 0.4310 98 L 0.0813 0.5522 0.3665 99 M 0.0804 0.6008 0.3189 100 D 0.0745 0.6010 0.3245 101 A 0.0546 0.4840 0.4614 102 L 0.0549 0.3515 0.5936 103 K 0.0992 0.3033 0.5975 104 E 0.1353 0.2680 0.5967 105 E 0.0880 0.2413 0.6706 106 S 0.0619 0.2350 0.7032 107 E 0.0598 0.1597 0.7805 108 I 0.1043 0.0965 0.7992 109 I 0.2952 0.0516 0.6532 110 Y 0.4626 0.0096 0.5278 111 D 0.5861 0.0274 0.3865 112 F 0.9175 0.0046 0.0780 113 C 0.9240 0.0046 0.0715 114 M 0.9033 0.0073 0.0894 115 C 0.7015 0.0100 0.2884 116 N 0.1605 0.0147 0.8248 117 P 0.0772 0.0321 0.8906 118 P 0.0694 0.1328 0.7978 119 F 0.0954 0.1931 0.7115 120 F 0.1004 0.1631 0.7365 121 A 0.0631 0.2424 0.6945 122 N 0.0420 0.3641 0.5939 123 Q 0.0277 0.5030 0.4693 124 L 0.0267 0.6145 0.3587 125 E 0.0239 0.6714 0.3047 126 A 0.0266 0.6627 0.3107 127 K 0.0307 0.6189 0.3504 128 G 0.0411 0.5348 0.4241 129 V 0.0524 0.5038 0.4438 130 N 0.0340 0.6794 0.2866 131 S 0.0473 0.7274 0.2252 132 R 0.0451 0.7637 0.1911 133 N 0.0486 0.7442 0.2072 134 P 0.0461 0.7110 0.2429 135 R 0.0419 0.6371 0.3211 136 R 0.0562 0.4863 0.4575 137 P 0.0554 0.4154 0.5292 138 P 0.0423 0.5353 0.4224 139 P 0.0337 0.5964 0.3699 140 S 0.0509 0.6032 0.3459 141 S 0.0779 0.5273 0.3948 142 V 0.0901 0.3684 0.5415 143 N 0.0825 0.2215 0.6960 144 T 0.0875 0.1382 0.7742 145 G 0.1262 0.0926 0.7812 146 G 0.2644 0.0922 0.6435 147 I 0.5676 0.0841 0.3483 148 T 0.7303 0.0665 0.2032 149 E 0.8148 0.0547 0.1305 150 I 0.8383 0.0391 0.1226 151 M 0.7797 0.0355 0.1848 152 A 0.4971 0.0316 0.4714 153 E 0.0911 0.0637 0.8452 154 G 0.0287 0.1488 0.8225 155 G 0.0355 0.1760 0.7885 156 E 0.0394 0.4697 0.4909 157 L 0.0210 0.8481 0.1308 158 E 0.0143 0.9208 0.0649 159 F 0.0116 0.9345 0.0539 160 V 0.0084 0.9462 0.0454 161 K 0.0079 0.9495 0.0426 162 R 0.0055 0.9533 0.0411 163 I 0.0050 0.9528 0.0421 164 I 0.0049 0.9455 0.0496 165 H 0.0051 0.9313 0.0636 166 D 0.0070 0.8784 0.1146 167 S 0.0127 0.8321 0.1553 168 L 0.0087 0.8002 0.1911 169 Q 0.0124 0.7359 0.2516 170 L 0.0283 0.6318 0.3399 171 G 0.0511 0.4081 0.5408 172 K 0.0671 0.2501 0.6828 173 R 0.0782 0.1890 0.7328 174 L 0.1890 0.0620 0.7490 175 R 0.4240 0.0329 0.5431 176 W 0.8713 0.0092 0.1195 177 Y 0.8950 0.0091 0.0959 178 S 0.8812 0.0104 0.1083 179 C 0.7879 0.0200 0.1921 180 M 0.5834 0.0354 0.3812 181 L 0.2571 0.0854 0.6576 182 G 0.1094 0.1012 0.7895 183 K 0.0397 0.2954 0.6648 184 A 0.0352 0.4620 0.5029 185 C 0.0305 0.4915 0.4780 186 S 0.0340 0.4108 0.5552 187 L 0.0369 0.6898 0.2733 188 A 0.0284 0.8438 0.1278 189 P 0.0196 0.9074 0.0730 190 L 0.0183 0.9248 0.0570 191 K 0.0141 0.9345 0.0514 192 E 0.0097 0.9396 0.0507 193 E 0.0081 0.9267 0.0653 194 L 0.0092 0.8771 0.1138 195 R 0.0154 0.7353 0.2493 196 I 0.0347 0.4055 0.5598 197 Q 0.0616 0.1337 0.8047 198 G 0.0746 0.0917 0.8337 199 V 0.1933 0.0918 0.7148 200 P 0.4117 0.0784 0.5100 201 K 0.7050 0.0334 0.2616 202 V 0.7485 0.0240 0.2275 203 T 0.6695 0.0217 0.3088 204 Y 0.5010 0.0362 0.4628 205 T 0.2950 0.1211 0.5839 206 E 0.2815 0.2436 0.4749 207 F 0.2283 0.3342 0.4375 208 C 0.2164 0.2558 0.5279 209 Q 0.0917 0.1502 0.7580 210 G 0.0576 0.0569 0.8855 211 R 0.1861 0.0367 0.7772 212 T 0.5557 0.0277 0.4166 213 M 0.7473 0.0175 0.2353 214 R 0.8223 0.0176 0.1601 215 W 0.9025 0.0104 0.0871 216 A 0.9095 0.0125 0.0780 217 L 0.9015 0.0187 0.0798 218 A 0.8764 0.0232 0.1004 219 W 0.7713 0.0476 0.1810 220 S 0.5666 0.0868 0.3466 221 F 0.3324 0.0845 0.5831 222 Y 0.1632 0.0550 0.7818 223 D 0.0640 0.0207 0.9153