# This file is the result of combining several RDB files, specifically # T0194.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0194.t2k.stride-ebghtl.rdb (weight 1.24869) # T0194.t2k.str.rdb (weight 1.53983) # T0194.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 T0194.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0194 # 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 T0194.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 43 # # ============================================ # Comments from T0194.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0194 # 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 T0194.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 43 # # ============================================ # Comments from T0194.t2k.str.rdb # ============================================ # TARGET T0194 # 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 T0194.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 43 # # ============================================ # Comments from T0194.t2k.alpha.rdb # ============================================ # TARGET T0194 # 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 T0194.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 43 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0626 0.3522 0.5852 2 A 0.1059 0.5075 0.3867 3 N 0.0918 0.5506 0.3576 4 A 0.0688 0.5382 0.3931 5 P 0.0424 0.5831 0.3745 6 K 0.0488 0.4096 0.5416 7 G 0.0488 0.1286 0.8226 8 V 0.0944 0.0795 0.8262 9 K 0.1553 0.0321 0.8127 10 F 0.1322 0.0464 0.8215 11 S 0.1499 0.0689 0.7812 12 T 0.1599 0.0918 0.7483 13 S 0.1285 0.0651 0.8065 14 Q 0.1099 0.0327 0.8574 15 T 0.1012 0.0338 0.8650 16 T 0.0798 0.0422 0.8780 17 E 0.0075 0.8641 0.1284 18 E 0.0049 0.9278 0.0673 19 I 0.0046 0.9474 0.0480 20 V 0.0044 0.9556 0.0400 21 R 0.0044 0.9570 0.0386 22 A 0.0044 0.9560 0.0396 23 K 0.0045 0.9524 0.0432 24 V 0.0045 0.9481 0.0474 25 S 0.0045 0.9488 0.0466 26 E 0.0051 0.9279 0.0671 27 L 0.0068 0.8952 0.0980 28 V 0.0141 0.8231 0.1628 29 E 0.0227 0.5240 0.4532 30 Q 0.0383 0.1877 0.7739 31 Y 0.0853 0.0337 0.8810 32 D 0.0887 0.0396 0.8717 33 L 0.8350 0.0055 0.1595 34 I 0.9277 0.0037 0.0686 35 I 0.9314 0.0035 0.0651 36 G 0.9274 0.0041 0.0685 37 I 0.9059 0.0045 0.0895 38 P 0.8054 0.0069 0.1876 39 I 0.5094 0.0390 0.4516 40 D 0.1780 0.1417 0.6804 41 K 0.0357 0.3654 0.5989 42 E 0.0436 0.3332 0.6232 43 I 0.0877 0.3768 0.5355 44 S 0.0805 0.4357 0.4838 45 A 0.0611 0.6866 0.2523 46 S 0.0342 0.8563 0.1095 47 Y 0.0116 0.9251 0.0633 48 A 0.0081 0.9378 0.0540 49 N 0.0062 0.9443 0.0495 50 W 0.0044 0.9560 0.0396 51 K 0.0046 0.9550 0.0404 52 L 0.0049 0.9445 0.0506 53 V 0.0052 0.9337 0.0610 54 E 0.0065 0.9139 0.0796 55 K 0.0075 0.8415 0.1510 56 D 0.0161 0.6901 0.2938 57 Y 0.0683 0.3807 0.5511 58 A 0.0558 0.1488 0.7954 59 S 0.0972 0.0610 0.8419 60 K 0.2929 0.0376 0.6694 61 F 0.7914 0.0048 0.2038 62 H 0.9111 0.0037 0.0852 63 V 0.9047 0.0044 0.0910 64 L 0.8163 0.0116 0.1721 65 D 0.5006 0.0186 0.4808 66 A 0.1106 0.1881 0.7013 67 R 0.0493 0.3442 0.6065 68 A 0.0529 0.5560 0.3912 69 V 0.0487 0.6288 0.3224 70 E 0.0398 0.6431 0.3170 71 M 0.0207 0.7684 0.2109 72 I 0.0120 0.8529 0.1351 73 I 0.0073 0.9157 0.0769 74 D 0.0055 0.9354 0.0592 75 W 0.0056 0.9470 0.0475 76 L 0.0044 0.9576 0.0380 77 I 0.0044 0.9609 0.0348 78 N 0.0043 0.9611 0.0346 79 D 0.0044 0.9604 0.0353 80 I 0.0044 0.9595 0.0361 81 K 0.0044 0.9598 0.0359 82 G 0.0044 0.9574 0.0381 83 W 0.0045 0.9546 0.0409 84 L 0.0053 0.9414 0.0533 85 N 0.0055 0.8807 0.1138 86 T 0.0428 0.3312 0.6260 87 N 0.0272 0.0521 0.9207 88 P 0.0534 0.0724 0.8742 89 Y 0.0849 0.0690 0.8461 90 S 0.0767 0.0531 0.8702 91 R 0.0058 0.9007 0.0936 92 E 0.0046 0.9407 0.0547 93 G 0.0046 0.9504 0.0450 94 L 0.0044 0.9567 0.0389 95 D 0.0044 0.9587 0.0369 96 R 0.0044 0.9564 0.0392 97 F 0.0045 0.9528 0.0427 98 V 0.0046 0.9510 0.0444 99 E 0.0046 0.9488 0.0466 100 Q 0.0056 0.9135 0.0809 101 Y 0.0085 0.8744 0.1171 102 R 0.0209 0.7723 0.2068 103 K 0.0221 0.5436 0.4344 104 K 0.0554 0.2216 0.7230 105 T 0.2186 0.0548 0.7265 106 A 0.4657 0.0471 0.4872 107 A 0.8836 0.0086 0.1078 108 V 0.9206 0.0048 0.0746 109 L 0.9205 0.0050 0.0745 110 F 0.8903 0.0068 0.1029 111 V 0.7217 0.0314 0.2469 112 T 0.2877 0.1298 0.5824 113 D 0.1887 0.1360 0.6753 114 T 0.0509 0.5431 0.4061 115 K 0.0299 0.7165 0.2536 116 P 0.0390 0.7257 0.2353 117 L 0.0734 0.7114 0.2152 118 V 0.1460 0.5905 0.2635 119 A 0.1097 0.3834 0.5069 120 G 0.0998 0.1627 0.7375 121 G 0.1711 0.1027 0.7262 122 R 0.2619 0.1044 0.6337 123 L 0.1929 0.2277 0.5794 124 S 0.0649 0.3743 0.5608 125 N 0.0360 0.6602 0.3038 126 L 0.0403 0.8181 0.1415 127 K 0.0408 0.8721 0.0870 128 S 0.0898 0.8304 0.0798 129 F 0.0777 0.8520 0.0703 130 I 0.0446 0.8858 0.0697 131 I 0.0233 0.8795 0.0973 132 K 0.0261 0.8382 0.1358 133 S 0.0210 0.7982 0.1808 134 L 0.0788 0.4507 0.4706 135 K 0.0962 0.2809 0.6229 136 F 0.1987 0.2462 0.5551 137 H 0.2759 0.3916 0.3326 138 L 0.3715 0.4550 0.1736 139 L 0.3747 0.4491 0.1762 140 I 0.3806 0.4472 0.1722 141 S 0.3985 0.4210 0.1805 142 F 0.3823 0.3112 0.3065 143 L 0.4573 0.0913 0.4514 144 G 0.1064 0.0495 0.8441 145 E 0.0302 0.1327 0.8371 146 N 0.0521 0.0395 0.9083 147 G 0.0812 0.0444 0.8744 148 K 0.3641 0.0319 0.6041 149 L 0.7874 0.0180 0.1945 150 Q 0.6748 0.0396 0.2857 151 F 0.5262 0.2216 0.2522 152 F 0.3143 0.4195 0.2663 153 D 0.2794 0.4527 0.2678 154 K 0.1642 0.5490 0.2868 155 A 0.1683 0.4551 0.3766 156 R 0.0560 0.5013 0.4427 157 S 0.0432 0.4073 0.5494 158 A 0.0128 0.7155 0.2717 159 H 0.0057 0.9076 0.0866 160 D 0.0051 0.9318 0.0631 161 A 0.0045 0.9455 0.0501 162 H 0.0044 0.9569 0.0387 163 K 0.0044 0.9594 0.0363 164 L 0.0044 0.9589 0.0367 165 A 0.0044 0.9593 0.0363 166 V 0.0044 0.9597 0.0359 167 K 0.0044 0.9587 0.0369 168 F 0.0045 0.9536 0.0419 169 L 0.0048 0.9475 0.0478 170 K 0.0049 0.9354 0.0597 171 K 0.0073 0.8817 0.1110 172 Q 0.0170 0.7865 0.1965 173 L 0.0321 0.6549 0.3130 174 L 0.0277 0.5415 0.4308 175 K 0.0367 0.4298 0.5335 176 H 0.0508 0.2894 0.6599 177 S 0.0558 0.2060 0.7381 178 A 0.0871 0.1537 0.7592 179 K 0.0844 0.0978 0.8178 180 L 0.1969 0.0759 0.7273 181 K 0.4259 0.0650 0.5092 182 R 0.6026 0.0344 0.3630 183 G 0.7922 0.0147 0.1931 184 A 0.8907 0.0065 0.1028 185 F 0.9137 0.0055 0.0808 186 L 0.9130 0.0070 0.0799 187 T 0.8905 0.0097 0.0998 188 T 0.7779 0.0205 0.2016 189 V 0.4286 0.0451 0.5263 190 F 0.1299 0.0872 0.7829 191 D 0.0657 0.1054 0.8288 192 E 0.0282 0.4850 0.4868 193 Q 0.0119 0.7666 0.2215 194 T 0.0107 0.8156 0.1738 195 N 0.0072 0.8912 0.1016 196 T 0.0062 0.9250 0.0688 197 N 0.0057 0.9311 0.0632 198 L 0.0051 0.9373 0.0576 199 V 0.0045 0.9484 0.0471 200 Q 0.0047 0.9508 0.0446 201 E 0.0047 0.9465 0.0488 202 F 0.0050 0.9366 0.0584 203 D 0.0056 0.9106 0.0838 204 K 0.0091 0.8023 0.1886 205 L 0.0203 0.5990 0.3808 206 L 0.0458 0.3450 0.6092 207 D 0.0592 0.1847 0.7560 208 H 0.0816 0.1683 0.7501 209 S 0.1542 0.1638 0.6820 210 I 0.2941 0.1475 0.5584 211 N 0.4662 0.1050 0.4288 212 I 0.5728 0.0876 0.3397 213 E 0.6450 0.0934 0.2616 214 Q 0.7058 0.0786 0.2156 215 S 0.6769 0.0534 0.2697 216 L 0.5870 0.0766 0.3364 217 L 0.3840 0.0923 0.5237 218 S 0.2171 0.1473 0.6356 219 P 0.3195 0.2078 0.4727 220 V 0.5619 0.2279 0.2102 221 I 0.6145 0.2547 0.1308 222 C 0.7056 0.1793 0.1152 223 T 0.6600 0.1872 0.1527 224 H 0.6078 0.1513 0.2409 225 T 0.4147 0.1442 0.4411 226 G 0.1613 0.0296 0.8091 227 L 0.0265 0.1082 0.8652 228 N 0.0434 0.0554 0.9012 229 S 0.4805 0.0191 0.5003 230 Y 0.8390 0.0059 0.1551 231 V 0.9195 0.0041 0.0764 232 I 0.9234 0.0040 0.0726 233 V 0.9130 0.0049 0.0821 234 L 0.8635 0.0067 0.1298 235 Q 0.7276 0.0144 0.2580 236 G 0.3158 0.0282 0.6559 237 E 0.0450 0.0370 0.9180