--- /dev/null
+HEADER OXIDOREDUCTASE/ELECTRON TRANSPORT 08-MAY-00 1GAQ \r
+ATOM 2 CA GLU A 19 20.491 30.713 36.290 1.00 74.29 C \r
+ATOM 11 CA SER A 20 24.056 29.774 37.264 1.00 72.09 C \r
+ATOM 17 CA LYS A 21 27.517 31.289 37.563 1.00 70.09 C \r
+ATOM 26 CA LYS A 22 28.794 27.865 36.481 1.00 68.64 C \r
+ATOM 35 CA GLN A 23 29.484 26.806 32.884 1.00 70.46 C \r
+ATOM 44 CA GLU A 24 26.420 25.175 31.360 1.00 72.08 C \r
+ATOM 53 CA GLU A 25 26.736 26.049 27.683 1.00 70.43 C \r
+ATOM 62 CA GLY A 26 28.299 22.912 26.233 1.00 63.14 C \r
+ATOM 66 CA VAL A 27 26.863 20.704 28.982 1.00 54.50 C \r
+ATOM 73 CA VAL A 28 25.030 17.390 28.655 1.00 48.32 C \r
+ATOM 80 CA THR A 29 23.728 14.677 30.991 1.00 44.86 C \r
+ATOM 87 CA ASN A 30 22.327 11.164 30.703 1.00 45.42 C \r
+ATOM 95 CA LEU A 31 23.332 10.459 27.102 1.00 45.42 C \r
+ATOM 103 CA TYR A 32 23.549 6.898 28.380 1.00 45.88 C \r
+ATOM 115 CA LYS A 33 21.656 5.321 31.262 1.00 47.27 C \r
+ATOM 124 CA PRO A 34 21.991 2.046 33.248 1.00 48.99 C \r
+ATOM 131 CA LYS A 35 19.339 0.560 30.970 1.00 52.75 C \r
+ATOM 140 CA GLU A 36 21.580 0.855 27.886 1.00 53.33 C \r
+ATOM 149 CA PRO A 37 25.154 2.015 28.678 1.00 47.54 C \r
+ATOM 156 CA TYR A 38 27.929 2.872 26.249 1.00 41.98 C \r
+ATOM 168 CA VAL A 39 30.355 -0.017 25.909 1.00 41.48 C \r
+ATOM 175 CA GLY A 40 33.823 1.485 25.966 1.00 37.59 C \r
+ATOM 179 CA ARG A 41 37.165 -0.277 26.122 1.00 39.77 C \r
+ATOM 190 CA CYS A 42 40.148 -0.029 28.442 1.00 36.51 C \r
+ATOM 196 CA LEU A 43 43.095 1.441 26.554 1.00 36.13 C \r
+ATOM 204 CA LEU A 44 45.231 2.023 29.649 1.00 33.55 C \r
+ATOM 212 CA ASN A 45 45.140 1.026 33.307 1.00 27.79 C \r
+ATOM 220 CA THR A 46 48.056 1.800 35.617 1.00 28.75 C \r
+ATOM 227 CA LYS A 47 48.542 1.776 39.388 1.00 30.31 C \r
+ATOM 236 CA ILE A 48 49.564 5.317 40.376 1.00 31.32 C \r
+ATOM 244 CA THR A 49 50.339 4.682 44.059 1.00 37.62 C \r
+ATOM 251 CA GLY A 50 53.585 3.317 45.460 1.00 44.49 C \r
+ATOM 255 CA ASP A 51 53.706 -0.448 46.087 1.00 52.89 C \r
+ATOM 263 CA ASP A 52 53.910 0.545 49.751 1.00 55.23 C \r
+ATOM 271 CA ALA A 53 50.816 2.767 50.056 1.00 53.34 C \r
+ATOM 276 CA PRO A 54 47.904 1.940 52.405 1.00 50.60 C \r
+ATOM 283 CA GLY A 55 45.420 1.579 49.561 1.00 50.35 C \r
+ATOM 287 CA GLU A 56 46.098 1.286 45.836 1.00 42.53 C \r
+ATOM 296 CA THR A 57 44.534 3.816 43.480 1.00 41.14 C \r
+ATOM 303 CA TRP A 58 44.540 3.423 39.708 1.00 35.60 C \r
+ATOM 317 CA HIS A 59 44.468 5.853 36.796 1.00 31.89 C \r
+ATOM 327 CA MET A 60 42.658 4.227 33.866 1.00 31.65 C \r
+ATOM 335 CA VAL A 61 41.716 5.345 30.350 1.00 30.43 C \r
+ATOM 342 CA PHE A 62 38.669 4.172 28.360 1.00 34.36 C \r
+ATOM 353 CA SER A 63 37.657 4.908 24.772 1.00 34.69 C \r
+ATOM 359 CA THR A 64 34.448 6.828 23.951 1.00 36.96 C \r
+ATOM 366 CA GLU A 65 34.691 7.644 20.254 1.00 40.08 C \r
+ATOM 375 CA GLY A 66 33.742 11.183 21.285 1.00 40.22 C \r
+ATOM 379 CA LYS A 67 30.272 9.763 22.003 1.00 41.93 C \r
+ATOM 388 CA ILE A 68 30.279 11.116 25.577 1.00 41.52 C \r
+ATOM 396 CA PRO A 69 30.791 14.926 25.537 1.00 42.35 C \r
+ATOM 403 CA TYR A 70 31.228 15.232 29.299 1.00 39.84 C \r
+ATOM 415 CA ARG A 71 32.639 18.451 30.768 1.00 44.14 C \r
+ATOM 426 CA GLU A 72 35.122 19.278 33.515 1.00 43.82 C \r
+ATOM 435 CA GLY A 73 33.472 18.458 36.835 1.00 41.97 C \r
+ATOM 439 CA GLN A 74 30.929 15.874 35.657 1.00 37.19 C \r
+ATOM 448 CA SER A 75 31.285 12.124 36.138 1.00 38.28 C \r
+ATOM 454 CA ILE A 76 30.458 8.792 34.539 1.00 36.84 C \r
+ATOM 462 CA GLY A 77 28.983 5.620 35.918 1.00 35.39 C \r
+ATOM 466 CA VAL A 78 30.311 2.108 35.530 1.00 32.05 C \r
+ATOM 473 CA ILE A 79 28.458 -1.201 35.591 1.00 32.67 C \r
+ATOM 481 CA ALA A 80 30.745 -4.018 36.644 1.00 35.36 C \r
+ATOM 486 CA ASP A 81 30.359 -7.373 34.872 1.00 38.72 C \r
+ATOM 494 CA GLY A 82 28.308 -10.332 36.110 1.00 45.79 C \r
+ATOM 498 CA VAL A 83 25.820 -10.242 39.001 1.00 52.24 C \r
+ATOM 505 CA ASP A 84 25.838 -10.250 42.834 1.00 60.54 C \r
+ATOM 513 CA LYS A 85 25.014 -13.158 45.196 1.00 66.72 C \r
+ATOM 522 CA ASN A 86 21.414 -13.062 43.904 1.00 67.37 C \r
+ATOM 530 CA GLY A 87 21.724 -13.423 40.136 1.00 64.74 C \r
+ATOM 534 CA LYS A 88 20.971 -9.733 39.570 1.00 61.12 C \r
+ATOM 543 CA PRO A 89 23.054 -7.201 37.561 1.00 54.68 C \r
+ATOM 550 CA HIS A 90 25.224 -4.957 39.755 1.00 44.44 C \r
+ATOM 560 CA LYS A 91 23.940 -1.433 40.260 1.00 40.48 C \r
+ATOM 569 CA VAL A 92 25.803 1.546 38.843 1.00 38.45 C \r
+ATOM 576 CA ARG A 93 28.709 2.986 40.828 1.00 38.93 C \r
+ATOM 587 CA LEU A 94 29.778 6.584 40.096 1.00 34.37 C \r
+ATOM 595 CA TYR A 95 33.309 7.878 39.513 1.00 30.27 C \r
+ATOM 607 CA SER A 96 34.425 11.475 39.057 1.00 29.44 C \r
+ATOM 613 CA ILE A 97 36.029 12.090 35.662 1.00 27.61 C \r
+ATOM 621 CA ALA A 98 39.769 12.693 36.069 1.00 31.12 C \r
+ATOM 626 CA SER A 99 40.393 13.712 32.475 1.00 32.42 C \r
+ATOM 632 CA SER A 100 39.566 17.142 31.059 1.00 36.14 C \r
+ATOM 638 CA ALA A 101 37.097 17.367 28.154 1.00 41.07 C \r
+ATOM 643 CA ILE A 102 39.764 16.549 25.527 1.00 47.65 C \r
+ATOM 651 CA GLY A 103 41.172 13.692 27.599 1.00 46.77 C \r
+ATOM 655 CA ASP A 104 44.730 12.612 28.289 1.00 43.82 C \r
+ATOM 663 CA PHE A 105 45.115 12.065 24.522 1.00 41.52 C \r
+ATOM 674 CA GLY A 106 43.862 15.455 23.328 1.00 41.66 C \r
+ATOM 678 CA ASP A 107 41.355 13.883 20.926 1.00 40.90 C \r
+ATOM 686 CA SER A 108 38.132 14.250 22.954 1.00 42.95 C \r
+ATOM 692 CA LYS A 109 37.967 10.535 22.224 1.00 44.74 C \r
+ATOM 701 CA THR A 110 38.731 9.184 25.704 1.00 41.09 C \r
+ATOM 708 CA VAL A 111 37.728 9.519 29.374 1.00 39.03 C \r
+ATOM 715 CA SER A 112 39.912 8.705 32.399 1.00 37.17 C \r
+ATOM 721 CA LEU A 113 39.098 7.476 35.935 1.00 32.10 C \r
+ATOM 729 CA CYS A 114 40.964 7.578 39.261 1.00 30.65 C \r
+ATOM 735 CA VAL A 115 39.724 4.459 41.060 1.00 33.45 C \r
+ATOM 742 CA LYS A 116 40.668 3.524 44.628 1.00 34.75 C \r
+ATOM 751 CA ARG A 117 40.376 -0.250 45.123 1.00 32.85 C \r
+ATOM 762 CA LEU A 118 38.137 -1.094 48.077 1.00 30.50 C \r
+ATOM 770 CA ILE A 119 39.376 -3.752 50.459 1.00 34.34 C \r
+ATOM 778 CA TYR A 120 38.699 -4.266 54.125 1.00 31.39 C \r
+ATOM 790 CA THR A 121 38.264 -7.086 56.567 1.00 28.83 C \r
+ATOM 797 CA ASN A 122 34.792 -7.477 58.109 1.00 26.51 C \r
+ATOM 805 CA ASP A 123 33.626 -8.382 61.634 1.00 31.58 C \r
+ATOM 813 CA ALA A 124 34.191 -12.077 60.901 1.00 27.84 C \r
+ATOM 818 CA GLY A 125 37.759 -11.844 59.728 1.00 32.39 C \r
+ATOM 822 CA GLU A 126 36.809 -12.146 56.073 1.00 35.82 C \r
+ATOM 831 CA ILE A 127 38.655 -9.932 53.598 1.00 38.42 C \r
+ATOM 839 CA VAL A 128 36.025 -8.261 51.421 1.00 33.73 C \r
+ATOM 846 CA LYS A 129 36.482 -6.484 48.090 1.00 31.87 C \r
+ATOM 855 CA GLY A 130 34.363 -3.680 46.686 1.00 26.91 C \r
+ATOM 859 CA VAL A 131 32.680 -5.051 43.569 1.00 27.89 C \r
+ATOM 866 CA CYS A 132 33.074 -2.246 41.018 1.00 28.46 C \r
+ATOM 872 CA SER A 133 36.266 -0.553 42.213 1.00 31.33 C \r
+ATOM 878 CA ASN A 134 37.861 -3.983 41.984 1.00 30.29 C \r
+ATOM 886 CA PHE A 135 36.318 -4.795 38.623 1.00 31.48 C \r
+ATOM 897 CA LEU A 136 37.926 -1.553 37.520 1.00 27.81 C \r
+ATOM 905 CA CYS A 137 41.417 -1.976 38.955 1.00 25.91 C \r
+ATOM 911 CA ASP A 138 41.605 -5.419 37.338 1.00 30.22 C \r
+ATOM 919 CA LEU A 139 40.462 -4.306 33.874 1.00 32.69 C \r
+ATOM 927 CA GLN A 140 42.851 -5.511 31.186 1.00 36.80 C \r
+ATOM 936 CA PRO A 141 43.380 -3.220 28.170 1.00 36.16 C \r
+ATOM 943 CA GLY A 142 40.864 -4.420 25.586 1.00 31.10 C \r
+ATOM 947 CA ASP A 143 38.129 -5.298 28.055 1.00 30.62 C \r
+ATOM 955 CA ASN A 144 34.690 -3.847 27.645 1.00 33.52 C \r
+ATOM 963 CA VAL A 145 33.430 -1.522 30.361 1.00 37.08 C \r
+ATOM 970 CA GLN A 146 29.817 -0.374 30.523 1.00 37.65 C \r
+ATOM 979 CA ILE A 147 29.547 3.413 31.045 1.00 30.95 C \r
+ATOM 987 CA THR A 148 26.637 5.791 31.832 1.00 29.95 C \r
+ATOM 994 CA GLY A 149 26.297 9.581 31.843 1.00 32.81 C \r
+ATOM 998 CA PRO A 150 27.785 12.148 31.800 1.00 34.98 C \r
+ATOM 1005 CA VAL A 151 26.376 12.668 35.275 1.00 36.53 C \r
+ATOM 1012 CA GLY A 152 26.196 15.756 37.474 1.00 43.09 C \r
+ATOM 1016 CA LYS A 153 26.048 19.528 37.068 1.00 48.37 C \r
+ATOM 1025 CA GLU A 154 26.921 20.540 40.633 1.00 49.70 C \r
+ATOM 1034 CA MET A 155 30.710 20.266 40.235 1.00 47.30 C \r
+ATOM 1042 CA LEU A 156 30.882 22.020 36.869 1.00 50.36 C \r
+ATOM 1050 CA MET A 157 33.362 24.883 36.404 1.00 55.29 C \r
+ATOM 1058 CA PRO A 158 32.521 28.612 36.605 1.00 54.88 C \r
+ATOM 1065 CA LYS A 159 32.291 30.776 33.464 1.00 54.92 C \r
+ATOM 1074 CA ASP A 160 34.497 33.503 34.939 1.00 57.22 C \r
+ATOM 1082 CA PRO A 161 38.055 32.687 33.759 1.00 58.62 C \r
+ATOM 1089 CA ASN A 162 39.524 35.240 36.163 1.00 60.44 C \r
+ATOM 1097 CA ALA A 163 37.814 33.910 39.279 1.00 55.80 C \r
+ATOM 1102 CA THR A 164 39.596 32.487 42.316 1.00 51.04 C \r
+ATOM 1109 CA ILE A 165 38.966 28.771 42.756 1.00 50.26 C \r
+ATOM 1117 CA ILE A 166 39.774 26.773 45.885 1.00 47.54 C \r
+ATOM 1125 CA MET A 167 39.883 23.014 45.324 1.00 46.38 C \r
+ATOM 1133 CA LEU A 168 39.700 20.963 48.522 1.00 42.18 C \r
+ATOM 1141 CA ALA A 169 40.377 17.316 47.770 1.00 36.41 C \r
+ATOM 1146 CA THR A 170 41.005 14.086 49.622 1.00 32.98 C \r
+ATOM 1153 CA GLY A 171 42.027 10.802 48.014 1.00 31.36 C \r
+ATOM 1157 CA THR A 172 40.386 10.037 44.680 1.00 30.48 C \r
+ATOM 1164 CA GLY A 173 38.640 13.335 45.359 1.00 33.99 C \r
+ATOM 1168 CA ILE A 174 41.418 15.036 43.394 1.00 35.66 C \r
+ATOM 1176 CA ALA A 175 39.758 13.585 40.300 1.00 36.00 C \r
+ATOM 1181 CA PRO A 176 37.445 16.385 39.155 1.00 39.41 C \r
+ATOM 1188 CA PHE A 177 40.109 18.971 39.976 1.00 43.21 C \r
+ATOM 1199 CA ARG A 178 42.726 17.119 37.955 1.00 41.09 C \r
+ATOM 1210 CA SER A 179 40.235 17.536 35.124 1.00 39.92 C \r
+ATOM 1216 CA PHE A 180 39.808 21.204 36.009 1.00 39.23 C \r
+ATOM 1227 CA LEU A 181 43.528 21.949 35.995 1.00 39.50 C \r
+ATOM 1235 CA TRP A 182 44.305 20.081 32.770 1.00 41.47 C \r
+ATOM 1249 CA LYS A 183 42.141 22.654 30.972 1.00 48.08 C \r
+ATOM 1258 CA MET A 184 43.477 25.547 33.062 1.00 52.79 C \r
+ATOM 1266 CA PHE A 185 47.102 25.043 32.014 1.00 57.35 C \r
+ATOM 1277 CA PHE A 186 48.075 21.921 30.051 1.00 55.98 C \r
+ATOM 1288 CA GLU A 187 45.758 23.173 27.297 1.00 54.44 C \r
+ATOM 1297 CA LYS A 188 44.908 26.236 25.196 1.00 51.29 C \r
+ATOM 1306 CA HIS A 189 41.395 27.080 24.003 1.00 51.35 C \r
+ATOM 1316 CA ASP A 190 40.108 29.972 21.873 1.00 54.30 C \r
+ATOM 1324 CA ASP A 191 37.199 30.481 24.249 1.00 53.95 C \r
+ATOM 1332 CA TYR A 192 38.816 29.937 27.634 1.00 50.68 C \r
+ATOM 1344 CA LYS A 193 41.916 31.388 29.230 1.00 51.00 C \r
+ATOM 1353 CA PHE A 194 42.322 30.967 32.956 1.00 52.09 C \r
+ATOM 1364 CA ASN A 195 43.672 34.234 34.312 1.00 56.46 C \r
+ATOM 1372 CA GLY A 196 42.616 34.078 37.969 1.00 57.17 C \r
+ATOM 1376 CA LEU A 197 43.874 31.920 40.843 1.00 57.92 C \r
+ATOM 1384 CA GLY A 198 43.549 28.151 41.086 1.00 56.67 C \r
+ATOM 1388 CA TRP A 199 44.258 26.886 44.592 1.00 51.55 C \r
+ATOM 1402 CA LEU A 200 44.411 23.170 45.379 1.00 49.17 C \r
+ATOM 1410 CA PHE A 201 44.558 21.335 48.709 1.00 48.60 C \r
+ATOM 1421 CA LEU A 202 45.122 17.570 48.598 1.00 45.34 C \r
+ATOM 1429 CA GLY A 203 44.885 15.480 51.742 1.00 48.55 C \r
+ATOM 1433 CA VAL A 204 46.225 11.936 51.755 1.00 50.23 C \r
+ATOM 1440 CA PRO A 205 47.942 9.740 54.365 1.00 51.51 C \r
+ATOM 1447 CA THR A 206 51.284 9.148 52.648 1.00 50.21 C \r
+ATOM 1454 CA SER A 207 53.551 10.483 49.894 1.00 49.38 C \r
+ATOM 1460 CA SER A 208 53.267 7.061 48.259 1.00 43.49 C \r
+ATOM 1466 CA SER A 209 49.588 8.049 48.093 1.00 42.57 C \r
+ATOM 1472 CA LEU A 210 49.990 11.424 46.364 1.00 42.65 C \r
+ATOM 1480 CA LEU A 211 48.121 11.446 43.035 1.00 39.33 C \r
+ATOM 1488 CA TYR A 212 49.516 13.214 39.935 1.00 40.89 C \r
+ATOM 1500 CA LYS A 213 52.128 15.234 41.873 1.00 45.88 C \r
+ATOM 1509 CA GLU A 214 54.518 15.406 38.899 1.00 53.22 C \r
+ATOM 1518 CA GLU A 215 51.680 16.911 36.889 1.00 55.16 C \r
+ATOM 1527 CA PHE A 216 50.757 19.475 39.514 1.00 60.55 C \r
+ATOM 1538 CA GLY A 217 54.488 20.153 39.524 1.00 66.64 C \r
+ATOM 1542 CA LYS A 218 54.575 21.110 35.850 1.00 68.86 C \r
+ATOM 1551 CA MET A 219 51.398 23.159 36.265 1.00 66.97 C \r
+ATOM 1559 CA LYS A 220 53.138 25.090 39.061 1.00 65.97 C \r
+ATOM 1568 CA GLU A 221 55.654 26.250 36.459 1.00 70.02 C \r
+ATOM 1577 CA ARG A 222 53.584 26.507 33.294 1.00 73.48 C \r
+ATOM 1588 CA ALA A 223 52.005 29.449 35.175 1.00 76.21 C \r
+ATOM 1593 CA PRO A 224 53.272 29.877 38.804 1.00 79.25 C \r
+ATOM 1600 CA GLU A 225 51.296 33.124 39.020 1.00 81.84 C \r
+ATOM 1609 CA ASN A 226 47.873 31.528 38.622 1.00 78.84 C \r
+ATOM 1617 CA PHE A 227 48.418 28.176 40.350 1.00 75.28 C \r
+ATOM 1628 CA ARG A 228 49.090 27.305 43.996 1.00 72.05 C \r
+ATOM 1639 CA VAL A 229 49.165 23.724 45.323 1.00 68.82 C \r
+ATOM 1646 CA ASP A 230 49.258 22.581 48.958 1.00 66.54 C \r
+ATOM 1654 CA TYR A 231 49.605 18.943 49.968 1.00 60.31 C \r
+ATOM 1666 CA ALA A 232 48.551 17.560 53.332 1.00 57.39 C \r
+ATOM 1671 CA VAL A 233 50.260 14.228 53.945 1.00 57.14 C \r
+ATOM 1678 CA SER A 234 48.465 13.579 57.244 1.00 60.81 C \r
+ATOM 1684 CA ARG A 235 50.959 11.010 58.514 1.00 60.74 C \r
+ATOM 1695 CA GLU A 236 54.268 12.594 57.481 1.00 59.17 C \r
+ATOM 1704 CA GLN A 237 53.494 16.197 58.450 1.00 59.62 C \r
+ATOM 1713 CA THR A 238 52.590 18.236 61.521 1.00 63.18 C \r
+ATOM 1720 CA ASN A 239 52.019 21.937 62.188 1.00 66.71 C \r
+ATOM 1728 CA ALA A 240 52.096 23.767 65.537 1.00 70.06 C \r
+ATOM 1733 CA ALA A 241 51.302 21.400 68.410 1.00 72.44 C \r
+ATOM 1738 CA GLY A 242 52.383 18.324 66.438 1.00 72.38 C \r
+ATOM 1742 CA GLU A 243 48.826 18.169 65.110 1.00 69.71 C \r
+ATOM 1751 CA ARG A 244 48.674 15.776 62.148 1.00 67.21 C \r
+ATOM 1762 CA MET A 245 48.712 17.796 58.933 1.00 64.20 C \r
+ATOM 1770 CA TYR A 246 45.246 17.082 57.556 1.00 60.65 C \r
+ATOM 1782 CA ILE A 247 43.617 18.437 54.409 1.00 62.98 C \r
+ATOM 1790 CA GLN A 248 42.035 21.001 56.761 1.00 64.64 C \r
+ATOM 1799 CA THR A 249 45.057 21.461 59.009 1.00 63.37 C \r
+ATOM 1806 CA ARG A 250 46.891 22.664 55.903 1.00 62.47 C \r
+ATOM 1817 CA MET A 251 44.123 25.201 55.251 1.00 63.35 C \r
+ATOM 1825 CA ALA A 252 44.571 26.305 58.854 1.00 65.73 C \r
+ATOM 1830 CA GLU A 253 47.973 27.809 58.076 1.00 65.97 C \r
+ATOM 1839 CA TYR A 254 46.267 30.063 55.517 1.00 65.83 C \r
+ATOM 1851 CA LYS A 255 42.991 30.559 57.379 1.00 70.30 C \r
+ATOM 1860 CA GLU A 256 43.578 34.326 57.320 1.00 73.73 C \r
+ATOM 1869 CA GLU A 257 44.189 34.738 53.593 1.00 71.52 C \r
+ATOM 1878 CA LEU A 258 41.459 32.202 52.893 1.00 73.38 C \r
+ATOM 1886 CA TRP A 259 38.790 34.074 54.853 1.00 76.72 C \r
+ATOM 1900 CA GLU A 260 39.721 37.275 53.006 1.00 78.61 C \r
+ATOM 1909 CA LEU A 261 38.580 35.553 49.815 1.00 75.71 C \r
+ATOM 1917 CA LEU A 262 35.391 33.881 51.047 1.00 73.74 C \r
+ATOM 1925 CA LYS A 263 33.562 37.165 50.535 1.00 73.64 C \r
+ATOM 1934 CA LYS A 264 34.299 38.143 46.954 1.00 72.48 C \r
+ATOM 1943 CA ASP A 265 31.954 37.554 43.993 1.00 69.65 C \r
+ATOM 1951 CA ASN A 266 34.660 35.649 42.106 1.00 65.06 C \r
+ATOM 1959 CA THR A 267 35.835 33.117 44.683 1.00 58.24 C \r
+ATOM 1966 CA TYR A 268 34.459 29.646 43.909 1.00 51.04 C \r
+ATOM 1978 CA VAL A 269 35.192 26.827 46.382 1.00 44.95 C \r
+ATOM 1985 CA TYR A 270 35.012 23.150 45.368 1.00 44.96 C \r
+ATOM 1997 CA MET A 271 35.162 20.122 47.656 1.00 41.72 C \r
+ATOM 2005 CA CYS A 272 35.314 16.468 46.632 1.00 37.19 C \r
+ATOM 2011 CA GLY A 273 36.343 13.080 47.951 1.00 37.65 C \r
+ATOM 2015 CA LEU A 274 36.040 10.886 51.020 1.00 39.39 C \r
+ATOM 2023 CA LYS A 275 33.076 12.283 52.955 1.00 44.86 C \r
+ATOM 2032 CA GLY A 276 34.322 13.183 56.400 1.00 49.16 C \r
+ATOM 2036 CA MET A 277 36.932 15.608 55.168 1.00 53.30 C \r
+ATOM 2044 CA GLU A 278 33.917 17.921 55.165 1.00 56.74 C \r
+ATOM 2053 CA LYS A 279 33.531 18.089 58.947 1.00 59.30 C \r
+ATOM 2062 CA GLY A 280 36.982 19.413 59.776 1.00 58.94 C \r
+ATOM 2066 CA ILE A 281 36.705 22.048 57.063 1.00 61.43 C \r
+ATOM 2074 CA ASP A 282 33.453 23.402 58.515 1.00 67.06 C \r
+ATOM 2082 CA ASP A 283 35.050 23.189 61.972 1.00 74.12 C \r
+ATOM 2090 CA ILE A 284 37.991 25.422 61.040 1.00 78.49 C \r
+ATOM 2098 CA MET A 285 35.456 27.566 59.201 1.00 82.25 C \r
+ATOM 2106 CA VAL A 286 32.941 27.959 62.027 1.00 83.44 C \r
+ATOM 2113 CA SER A 287 35.610 29.113 64.469 1.00 83.43 C \r
+ATOM 2119 CA LEU A 288 36.927 31.601 61.887 1.00 85.53 C \r
+ATOM 2127 CA ALA A 289 33.506 33.025 60.970 1.00 86.85 C \r
+ATOM 2132 CA GLU A 290 31.841 32.696 64.387 1.00 89.26 C \r
+ATOM 2141 CA LYS A 291 34.438 35.312 65.347 1.00 88.73 C \r
+ATOM 2150 CA ASP A 292 33.635 37.891 62.652 1.00 88.03 C \r
+ATOM 2158 CA GLY A 293 30.219 37.450 61.081 1.00 87.88 C \r
+ATOM 2162 CA ILE A 294 27.319 35.051 61.511 1.00 84.61 C \r
+ATOM 2170 CA ASP A 295 27.665 31.329 62.188 1.00 82.45 C \r
+ATOM 2178 CA TRP A 296 29.539 29.627 59.355 1.00 80.12 C \r
+ATOM 2192 CA PHE A 297 26.527 27.452 58.512 1.00 78.99 C \r
+ATOM 2203 CA ASP A 298 24.167 30.241 57.486 1.00 76.37 C \r
+ATOM 2211 CA TYR A 299 27.074 31.748 55.561 1.00 74.07 C \r
+ATOM 2223 CA LYS A 300 27.679 28.620 53.473 1.00 74.31 C \r
+ATOM 2232 CA LYS A 301 24.059 29.146 52.464 1.00 75.97 C \r
+ATOM 2241 CA GLN A 302 24.921 32.563 51.018 1.00 75.38 C \r
+ATOM 2250 CA LEU A 303 27.896 31.099 49.155 1.00 72.10 C \r
+ATOM 2258 CA LYS A 304 25.917 28.207 47.690 1.00 72.08 C \r
+ATOM 2267 CA ARG A 305 23.595 31.021 46.594 1.00 74.82 C \r
+ATOM 2278 CA GLY A 306 26.071 32.136 43.958 1.00 71.84 C \r
+ATOM 2282 CA ASP A 307 27.505 28.682 43.220 1.00 67.23 C \r
+ATOM 2290 CA GLN A 308 30.620 29.291 45.346 1.00 60.18 C \r
+ATOM 2299 CA TRP A 309 30.585 26.177 47.537 1.00 52.25 C \r
+ATOM 2313 CA ASN A 310 29.894 22.997 45.597 1.00 45.03 C \r
+ATOM 2321 CA VAL A 311 30.327 19.716 47.403 1.00 39.13 C \r
+ATOM 2328 CA GLU A 312 30.507 16.190 46.110 1.00 35.17 C \r
+ATOM 2337 CA VAL A 313 31.761 13.957 48.861 1.00 30.12 C \r
+ATOM 2344 CA TYR A 314 31.112 10.230 49.021 1.00 28.23 C \r
+ATOM 2358 CA ALA B 1 2.311 24.702 44.475 1.00 74.17 C \r
+ATOM 2363 CA THR B 2 3.590 24.207 48.055 1.00 74.76 C \r
+ATOM 2370 CA TYR B 3 3.069 20.876 49.837 1.00 73.52 C \r
+ATOM 2382 CA ASN B 4 3.748 19.874 53.435 1.00 75.75 C \r
+ATOM 2390 CA VAL B 5 6.618 17.399 53.868 1.00 75.95 C \r
+ATOM 2397 CA LYS B 6 7.769 15.523 56.983 1.00 77.70 C \r
+ATOM 2406 CA LEU B 7 11.351 14.325 57.458 1.00 78.91 C \r
+ATOM 2414 CA ILE B 8 11.807 11.511 59.985 1.00 81.00 C \r
+ATOM 2422 CA THR B 9 15.560 12.046 60.247 1.00 87.49 C \r
+ATOM 2429 CA PRO B 10 17.662 9.793 62.539 1.00 92.94 C \r
+ATOM 2436 CA GLU B 11 18.161 13.147 64.282 1.00 96.61 C \r
+ATOM 2445 CA GLY B 12 14.579 14.154 65.041 1.00 97.52 C \r
+ATOM 2449 CA GLU B 13 11.602 14.823 62.748 1.00 96.90 C \r
+ATOM 2458 CA VAL B 14 11.547 17.892 60.480 1.00 96.63 C \r
+ATOM 2465 CA GLU B 15 8.340 19.701 59.440 1.00 94.86 C \r
+ATOM 2474 CA LEU B 16 9.471 21.479 56.254 1.00 91.55 C \r
+ATOM 2482 CA GLN B 17 7.281 23.141 53.598 1.00 89.75 C \r
+ATOM 2491 CA VAL B 18 8.485 22.069 50.145 1.00 87.92 C \r
+ATOM 2498 CA PRO B 19 6.906 23.558 46.964 1.00 86.35 C \r
+ATOM 2505 CA ASP B 20 5.990 21.744 43.717 1.00 86.29 C \r
+ATOM 2513 CA ASP B 21 8.578 22.751 41.083 1.00 83.78 C \r
+ATOM 2521 CA VAL B 22 11.385 22.401 43.639 1.00 80.98 C \r
+ATOM 2528 CA TYR B 23 13.439 19.280 44.481 1.00 77.04 C \r
+ATOM 2540 CA ILE B 24 13.212 18.196 48.120 1.00 76.45 C \r
+ATOM 2548 CA LEU B 25 16.959 18.133 48.851 1.00 75.15 C \r
+ATOM 2556 CA ASP B 26 17.154 21.745 47.689 1.00 75.80 C \r
+ATOM 2564 CA GLN B 27 14.616 22.906 50.280 1.00 76.31 C \r
+ATOM 2573 CA ALA B 28 16.562 20.957 52.914 1.00 78.86 C \r
+ATOM 2578 CA GLU B 29 19.698 23.011 52.198 1.00 81.51 C \r
+ATOM 2587 CA GLU B 30 17.491 26.106 52.510 1.00 83.25 C \r
+ATOM 2596 CA ASP B 31 15.857 25.933 55.935 1.00 81.92 C \r
+ATOM 2604 CA GLY B 32 19.280 24.859 57.151 1.00 79.08 C \r
+ATOM 2608 CA ILE B 33 18.621 21.130 57.157 1.00 76.93 C \r
+ATOM 2616 CA ASP B 34 21.528 18.731 56.618 1.00 73.53 C \r
+ATOM 2624 CA LEU B 35 20.738 15.738 54.421 1.00 67.74 C \r
+ATOM 2632 CA PRO B 36 23.138 13.391 52.547 1.00 65.90 C \r
+ATOM 2639 CA TYR B 37 23.916 14.226 48.912 1.00 64.85 C \r
+ATOM 2651 CA SER B 38 26.659 13.373 46.412 1.00 62.58 C \r
+ATOM 2657 CA CYS B 39 26.193 13.603 42.652 1.00 60.99 C \r
+ATOM 2663 CA ARG B 40 22.908 15.441 43.251 1.00 58.35 C \r
+ATOM 2674 CA ALA B 41 21.699 14.108 39.886 1.00 56.38 C \r
+ATOM 2679 CA GLY B 42 19.886 10.955 40.991 1.00 56.66 C \r
+ATOM 2683 CA SER B 43 22.465 8.336 40.010 1.00 58.55 C \r
+ATOM 2689 CA CYS B 44 23.548 7.052 43.447 1.00 56.27 C \r
+ATOM 2695 CA SER B 45 22.057 5.987 46.791 1.00 58.20 C \r
+ATOM 2701 CA SER B 46 23.574 8.773 48.890 1.00 59.13 C \r
+ATOM 2707 CA CYS B 47 20.220 10.475 49.517 1.00 65.64 C \r
+ATOM 2713 CA ALA B 48 17.911 7.436 49.610 1.00 69.71 C \r
+ATOM 2718 CA GLY B 49 14.733 7.635 51.681 1.00 73.09 C \r
+ATOM 2722 CA LYS B 50 11.712 5.340 52.183 1.00 73.77 C \r
+ATOM 2731 CA VAL B 51 8.551 7.412 51.568 1.00 76.51 C \r
+ATOM 2738 CA VAL B 52 5.237 7.081 53.429 1.00 78.85 C \r
+ATOM 2745 CA SER B 53 2.180 9.376 53.647 1.00 79.57 C \r
+ATOM 2751 CA GLY B 54 2.118 10.991 50.218 1.00 76.32 C \r
+ATOM 2755 CA SER B 55 3.577 10.944 46.726 1.00 76.31 C \r
+ATOM 2761 CA VAL B 56 6.436 12.592 44.828 1.00 77.50 C \r
+ATOM 2768 CA ASP B 57 7.691 12.960 41.243 1.00 76.83 C \r
+ATOM 2776 CA GLN B 58 11.150 11.483 40.555 1.00 76.66 C \r
+ATOM 2785 CA SER B 59 10.976 10.827 36.792 1.00 80.19 C \r
+ATOM 2791 CA ASP B 60 14.688 11.644 36.510 1.00 83.51 C \r
+ATOM 2799 CA GLN B 61 15.175 8.137 37.916 1.00 85.74 C \r
+ATOM 2808 CA SER B 62 18.644 7.080 36.699 1.00 85.85 C \r
+ATOM 2814 CA TYR B 63 19.324 5.049 39.852 1.00 84.49 C \r
+ATOM 2826 CA LEU B 64 15.683 4.296 40.629 1.00 89.06 C \r
+ATOM 2834 CA ASP B 65 15.356 0.604 39.742 1.00 92.21 C \r
+ATOM 2842 CA ASP B 66 12.421 -1.791 39.331 1.00 92.35 C \r
+ATOM 2850 CA GLY B 67 10.747 -2.542 42.659 1.00 89.07 C \r
+ATOM 2854 CA GLN B 68 12.336 0.632 44.010 1.00 88.41 C \r
+ATOM 2863 CA ILE B 69 9.483 2.828 42.742 1.00 86.11 C \r
+ATOM 2871 CA ALA B 70 7.060 0.441 44.446 1.00 81.10 C \r
+ATOM 2876 CA ASP B 71 8.985 -0.310 47.648 1.00 76.82 C \r
+ATOM 2884 CA GLY B 72 8.653 3.423 48.186 1.00 73.00 C \r
+ATOM 2888 CA TRP B 73 12.342 4.386 48.095 1.00 67.93 C \r
+ATOM 2902 CA VAL B 74 13.052 8.007 47.136 1.00 63.84 C \r
+ATOM 2909 CA LEU B 75 16.093 9.940 45.892 1.00 58.37 C \r
+ATOM 2917 CA THR B 76 15.524 13.198 47.826 1.00 55.82 C \r
+ATOM 2924 CA CYS B 77 17.941 15.109 45.556 1.00 58.23 C \r
+ATOM 2930 CA HIS B 78 15.777 14.389 42.513 1.00 64.55 C \r
+ATOM 2940 CA ALA B 79 12.108 14.429 43.512 1.00 68.40 C \r
+ATOM 2945 CA TYR B 80 9.442 17.152 43.581 1.00 69.69 C \r
+ATOM 2957 CA PRO B 81 6.414 16.584 45.842 1.00 71.39 C \r
+ATOM 2964 CA THR B 82 3.015 16.014 44.179 1.00 73.67 C \r
+ATOM 2971 CA SER B 83 1.278 15.771 47.557 1.00 76.90 C \r
+ATOM 2977 CA ASP B 84 1.940 16.119 51.289 1.00 75.20 C \r
+ATOM 2985 CA VAL B 85 4.840 13.765 52.050 1.00 71.37 C \r
+ATOM 2992 CA VAL B 86 6.363 11.824 54.956 1.00 70.12 C \r
+ATOM 2999 CA ILE B 87 9.770 10.300 54.188 1.00 74.18 C \r
+ATOM 3007 CA GLU B 88 12.211 8.403 56.410 1.00 78.53 C \r
+ATOM 3012 CA THR B 89 15.541 9.964 55.407 1.00 79.79 C \r
+ATOM 3019 CA HIS B 90 19.062 8.538 55.881 1.00 79.40 C \r
+ATOM 3029 CA LYS B 91 17.584 5.099 55.099 1.00 84.52 C \r
+ATOM 3038 CA GLU B 92 20.016 2.596 53.549 1.00 91.64 C \r
+ATOM 3047 CA GLU B 93 20.192 -0.858 51.981 1.00 98.97 C \r
+ATOM 3056 CA GLU B 94 23.321 -2.924 51.298 1.00106.32 C \r
+ATOM 3065 CA LEU B 95 22.104 -6.552 51.453 1.00111.32 C \r
+ATOM 3073 CA THR B 96 18.778 -8.417 51.866 1.00116.01 C \r
+ATOM 3080 CA GLY B 97 18.877 -11.302 49.394 1.00116.63 C \r
+ATOM 3084 CA ALA B 98 22.056 -9.833 47.910 1.00116.02 C \r
+ATOM 3091 CA GLU C 19 26.080 -2.480 15.294 1.00 73.96 C \r
+ATOM 3100 CA SER C 20 23.405 0.198 14.956 1.00 67.27 C \r
+ATOM 3106 CA LYS C 21 22.937 3.927 15.380 1.00 59.27 C \r
+ATOM 3115 CA LYS C 22 19.198 3.481 15.874 1.00 58.42 C \r
+ATOM 3124 CA GLN C 23 17.251 3.141 19.137 1.00 59.89 C \r
+ATOM 3133 CA GLU C 24 17.931 -0.276 20.610 1.00 62.66 C \r
+ATOM 3142 CA GLU C 25 16.850 -0.453 24.226 1.00 64.27 C \r
+ATOM 3151 CA GLY C 26 13.211 -0.817 25.116 1.00 61.78 C \r
+ATOM 3155 CA VAL C 27 12.703 -2.073 21.582 1.00 58.37 C \r
+ATOM 3162 CA VAL C 28 10.779 -5.347 21.485 1.00 54.17 C \r
+ATOM 3169 CA THR C 29 9.481 -7.339 18.549 1.00 52.79 C \r
+ATOM 3176 CA ASN C 30 6.670 -9.775 17.786 1.00 51.30 C \r
+ATOM 3184 CA LEU C 31 4.863 -9.997 21.112 1.00 51.05 C \r
+ATOM 3192 CA TYR C 32 1.766 -11.297 19.327 1.00 50.51 C \r
+ATOM 3204 CA LYS C 33 1.373 -13.532 16.266 1.00 49.49 C \r
+ATOM 3213 CA PRO C 34 -1.609 -14.150 13.925 1.00 50.98 C \r
+ATOM 3220 CA LYS C 35 -2.450 -17.248 16.011 1.00 55.46 C \r
+ATOM 3229 CA GLU C 36 -2.977 -15.400 19.288 1.00 53.79 C \r
+ATOM 3238 CA PRO C 37 -3.251 -11.638 18.607 1.00 49.32 C \r
+ATOM 3245 CA TYR C 38 -3.674 -9.050 21.318 1.00 46.76 C \r
+ATOM 3257 CA VAL C 39 -7.276 -7.947 21.418 1.00 43.68 C \r
+ATOM 3264 CA GLY C 40 -7.415 -4.194 21.922 1.00 41.62 C \r
+ATOM 3268 CA ARG C 41 -10.273 -1.719 21.954 1.00 40.07 C \r
+ATOM 3279 CA CYS C 42 -11.026 1.064 19.477 1.00 36.37 C \r
+ATOM 3285 CA LEU C 43 -11.330 4.206 21.583 1.00 31.09 C \r
+ATOM 3293 CA LEU C 44 -11.337 6.671 18.673 1.00 28.46 C \r
+ATOM 3301 CA ASN C 45 -11.792 6.653 14.923 1.00 26.74 C \r
+ATOM 3309 CA THR C 46 -11.954 9.920 13.013 1.00 25.29 C \r
+ATOM 3316 CA LYS C 47 -11.667 10.775 9.352 1.00 21.50 C \r
+ATOM 3325 CA ILE C 48 -8.895 13.355 9.121 1.00 19.33 C \r
+ATOM 3333 CA THR C 49 -9.125 14.281 5.442 1.00 20.38 C \r
+ATOM 3340 CA GLY C 50 -11.630 16.676 3.855 1.00 20.12 C \r
+ATOM 3344 CA ASP C 51 -14.895 15.345 2.412 1.00 21.75 C \r
+ATOM 3352 CA ASP C 52 -13.889 16.693 -0.999 1.00 21.19 C \r
+ATOM 3360 CA ALA C 53 -10.651 14.683 -0.749 1.00 21.06 C \r
+ATOM 3365 CA PRO C 54 -10.036 11.974 -3.413 1.00 21.39 C \r
+ATOM 3372 CA GLY C 55 -9.982 9.067 -0.977 1.00 24.42 C \r
+ATOM 3376 CA GLU C 56 -10.374 9.298 2.857 1.00 22.08 C \r
+ATOM 3385 CA THR C 57 -7.723 8.611 5.517 1.00 20.31 C \r
+ATOM 3392 CA TRP C 58 -8.541 7.849 9.162 1.00 19.33 C \r
+ATOM 3406 CA HIS C 59 -6.758 8.520 12.438 1.00 22.68 C \r
+ATOM 3416 CA MET C 60 -7.645 5.951 15.108 1.00 27.16 C \r
+ATOM 3424 CA VAL C 61 -6.672 5.224 18.723 1.00 29.32 C \r
+ATOM 3431 CA PHE C 62 -6.669 1.704 20.220 1.00 34.23 C \r
+ATOM 3442 CA SER C 63 -6.102 0.643 23.847 1.00 37.05 C \r
+ATOM 3448 CA THR C 64 -3.096 -1.517 24.798 1.00 41.86 C \r
+ATOM 3455 CA GLU C 65 -3.169 -1.652 28.621 1.00 48.33 C \r
+ATOM 3464 CA GLY C 66 0.537 -0.885 28.318 1.00 52.45 C \r
+ATOM 3468 CA LYS C 67 0.955 -4.385 26.891 1.00 54.14 C \r
+ATOM 3477 CA ILE C 68 2.429 -3.211 23.570 1.00 51.52 C \r
+ATOM 3485 CA PRO C 69 5.602 -1.279 24.487 1.00 49.85 C \r
+ATOM 3492 CA TYR C 70 6.523 -0.180 20.967 1.00 44.48 C \r
+ATOM 3504 CA ARG C 71 9.185 2.353 19.993 1.00 40.96 C \r
+ATOM 3515 CA GLU C 72 8.727 5.317 17.688 1.00 33.49 C \r
+ATOM 3524 CA GLY C 73 8.913 3.876 14.164 1.00 30.16 C \r
+ATOM 3528 CA GLN C 74 7.423 0.399 14.427 1.00 31.26 C \r
+ATOM 3537 CA SER C 75 4.187 -0.913 12.966 1.00 33.65 C \r
+ATOM 3543 CA ILE C 76 1.454 -3.212 14.278 1.00 33.75 C \r
+ATOM 3551 CA GLY C 77 -0.295 -5.923 12.356 1.00 34.32 C \r
+ATOM 3555 CA VAL C 78 -4.060 -6.111 12.164 1.00 36.67 C \r
+ATOM 3562 CA ILE C 79 -6.137 -9.230 11.507 1.00 41.91 C \r
+ATOM 3570 CA ALA C 80 -9.427 -8.086 10.024 1.00 44.06 C \r
+ATOM 3575 CA ASP C 81 -12.530 -9.927 11.224 1.00 47.03 C \r
+ATOM 3583 CA GLY C 82 -13.972 -12.487 8.829 1.00 53.52 C \r
+ATOM 3587 CA VAL C 83 -12.521 -14.951 6.324 1.00 62.57 C \r
+ATOM 3594 CA ASP C 84 -11.856 -14.200 2.630 1.00 71.97 C \r
+ATOM 3602 CA LYS C 85 -12.935 -17.403 0.861 1.00 76.86 C \r
+ATOM 3611 CA ASN C 86 -13.690 -18.960 4.253 1.00 76.52 C \r
+ATOM 3619 CA GLY C 87 -10.006 -19.837 4.066 1.00 76.22 C \r
+ATOM 3623 CA LYS C 88 -8.802 -19.138 7.616 1.00 71.60 C \r
+ATOM 3632 CA PRO C 89 -8.651 -15.577 8.944 1.00 64.14 C \r
+ATOM 3639 CA HIS C 90 -7.547 -12.649 6.805 1.00 52.35 C \r
+ATOM 3649 CA LYS C 91 -3.753 -12.529 6.474 1.00 46.81 C \r
+ATOM 3658 CA VAL C 92 -2.180 -9.868 8.686 1.00 43.48 C \r
+ATOM 3665 CA ARG C 93 -1.491 -6.414 7.232 1.00 36.99 C \r
+ATOM 3676 CA LEU C 94 0.983 -3.882 8.601 1.00 32.95 C \r
+ATOM 3684 CA TYR C 95 0.340 -0.239 9.510 1.00 24.84 C \r
+ATOM 3696 CA SER C 96 3.003 2.101 10.803 1.00 23.32 C \r
+ATOM 3702 CA ILE C 97 2.244 3.502 14.236 1.00 24.12 C \r
+ATOM 3710 CA ALA C 98 1.243 7.179 13.932 1.00 22.32 C \r
+ATOM 3715 CA SER C 99 1.572 7.636 17.676 1.00 25.69 C \r
+ATOM 3721 CA SER C 100 4.752 7.924 19.726 1.00 28.83 C \r
+ATOM 3727 CA ALA C 101 5.741 5.521 22.508 1.00 35.61 C \r
+ATOM 3732 CA ILE C 102 3.906 7.635 25.079 1.00 38.39 C \r
+ATOM 3740 CA GLY C 103 0.899 7.826 22.742 1.00 31.93 C \r
+ATOM 3744 CA ASP C 104 -1.803 10.384 21.986 1.00 28.77 C \r
+ATOM 3752 CA PHE C 105 -3.050 10.293 25.607 1.00 37.05 C \r
+ATOM 3763 CA GLY C 106 0.503 10.389 26.967 1.00 39.36 C \r
+ATOM 3767 CA ASP C 107 -0.221 7.437 29.266 1.00 41.44 C \r
+ATOM 3775 CA SER C 108 1.566 4.766 27.217 1.00 42.18 C \r
+ATOM 3781 CA LYS C 109 -1.747 2.877 27.156 1.00 42.45 C \r
+ATOM 3790 CA THR C 110 -2.698 3.586 23.515 1.00 38.10 C \r
+ATOM 3797 CA VAL C 111 -1.603 2.971 19.906 1.00 32.79 C \r
+ATOM 3804 CA SER C 112 -2.671 5.020 16.872 1.00 29.60 C \r
+ATOM 3810 CA LEU C 113 -2.713 4.324 13.126 1.00 25.68 C \r
+ATOM 3818 CA CYS C 114 -3.142 6.498 9.999 1.00 24.23 C \r
+ATOM 3824 CA VAL C 115 -5.345 4.496 7.641 1.00 22.80 C \r
+ATOM 3831 CA LYS C 116 -6.221 5.196 4.015 1.00 22.11 C \r
+ATOM 3840 CA ARG C 117 -9.458 3.521 2.955 1.00 25.68 C \r
+ATOM 3851 CA LEU C 118 -8.447 1.440 -0.100 1.00 28.80 C \r
+ATOM 3859 CA ILE C 119 -11.140 1.661 -2.792 1.00 31.75 C \r
+ATOM 3867 CA TYR C 120 -10.086 0.716 -6.312 1.00 32.93 C \r
+ATOM 3879 CA THR C 121 -11.388 -0.733 -9.598 1.00 36.84 C \r
+ATOM 3886 CA ASN C 122 -10.258 -4.257 -10.546 1.00 36.90 C \r
+ATOM 3894 CA ASP C 123 -9.574 -5.562 -14.056 1.00 45.45 C \r
+ATOM 3902 CA ALA C 124 -13.196 -6.758 -14.269 1.00 44.66 C \r
+ATOM 3907 CA GLY C 125 -14.207 -3.102 -14.023 1.00 45.49 C \r
+ATOM 3911 CA GLU C 126 -16.059 -3.511 -10.722 1.00 45.54 C \r
+ATOM 3920 CA ILE C 127 -15.507 -1.321 -7.638 1.00 39.70 C \r
+ATOM 3928 CA VAL C 128 -13.846 -3.171 -4.762 1.00 38.09 C \r
+ATOM 3935 CA LYS C 129 -12.759 -2.512 -1.198 1.00 33.77 C \r
+ATOM 3944 CA GLY C 130 -9.566 -3.363 0.599 1.00 31.98 C \r
+ATOM 3948 CA VAL C 131 -10.443 -5.797 3.385 1.00 33.16 C \r
+ATOM 3955 CA CYS C 132 -8.241 -4.645 6.257 1.00 29.97 C \r
+ATOM 3961 CA SER C 133 -8.238 -0.898 5.607 1.00 30.67 C \r
+ATOM 3967 CA ASN C 134 -12.022 -0.902 5.268 1.00 30.35 C \r
+ATOM 3975 CA PHE C 135 -12.375 -2.946 8.424 1.00 29.86 C \r
+ATOM 3986 CA LEU C 136 -10.223 -0.334 10.195 1.00 29.42 C \r
+ATOM 3994 CA CYS C 137 -11.779 2.834 8.813 1.00 32.27 C \r
+ATOM 4000 CA ASP C 138 -15.116 1.280 9.724 1.00 34.29 C \r
+ATOM 4008 CA LEU C 139 -14.287 0.699 13.399 1.00 37.51 C \r
+ATOM 4016 CA GLN C 140 -16.635 2.170 16.028 1.00 43.76 C \r
+ATOM 4025 CA PRO C 141 -15.630 3.032 19.581 1.00 42.77 C \r
+ATOM 4032 CA GLY C 142 -16.082 -0.210 21.478 1.00 42.83 C \r
+ATOM 4036 CA ASP C 143 -15.117 -2.625 18.696 1.00 40.91 C \r
+ATOM 4044 CA ASN C 144 -12.182 -4.947 19.288 1.00 45.66 C \r
+ATOM 4052 CA VAL C 145 -9.056 -5.146 17.145 1.00 46.95 C \r
+ATOM 4059 CA GLN C 146 -6.707 -8.107 16.606 1.00 48.69 C \r
+ATOM 4068 CA ILE C 147 -3.249 -6.538 17.123 1.00 46.84 C \r
+ATOM 4076 CA THR C 148 -0.010 -8.392 16.264 1.00 46.26 C \r
+ATOM 4083 CA GLY C 149 3.543 -7.117 16.634 1.00 45.60 C \r
+ATOM 4087 CA PRO C 150 5.248 -4.818 17.394 1.00 44.97 C \r
+ATOM 4094 CA VAL C 151 7.423 -5.293 14.321 1.00 44.50 C \r
+ATOM 4101 CA GLY C 152 10.289 -3.716 12.438 1.00 45.33 C \r
+ATOM 4105 CA LYS C 153 13.599 -2.161 13.435 1.00 48.64 C \r
+ATOM 4114 CA GLU C 154 14.166 -0.437 10.074 1.00 48.20 C \r
+ATOM 4123 CA MET C 155 12.437 2.888 10.737 1.00 41.77 C \r
+ATOM 4131 CA LEU C 156 13.839 3.081 14.267 1.00 38.27 C \r
+ATOM 4139 CA MET C 157 15.076 6.540 15.308 1.00 34.29 C \r
+ATOM 4147 CA PRO C 158 18.782 7.419 15.339 1.00 34.05 C \r
+ATOM 4154 CA LYS C 159 20.262 7.521 18.845 1.00 35.82 C \r
+ATOM 4163 CA ASP C 160 22.076 10.792 18.273 1.00 35.95 C \r
+ATOM 4171 CA PRO C 161 19.683 13.401 19.809 1.00 35.63 C \r
+ATOM 4178 CA ASN C 162 21.563 15.948 17.758 1.00 33.92 C \r
+ATOM 4186 CA ALA C 163 21.028 14.172 14.487 1.00 30.82 C \r
+ATOM 4191 CA THR C 164 19.693 15.722 11.305 1.00 25.18 C \r
+ATOM 4198 CA ILE C 165 16.617 13.601 10.636 1.00 19.91 C \r
+ATOM 4206 CA ILE C 166 15.351 13.978 7.060 1.00 13.76 C \r
+ATOM 4214 CA MET C 167 11.843 12.550 6.703 1.00 14.98 C \r
+ATOM 4222 CA LEU C 168 10.385 11.831 3.251 1.00 16.64 C \r
+ATOM 4230 CA ALA C 169 6.747 10.808 3.007 1.00 15.85 C \r
+ATOM 4235 CA THR C 170 3.765 10.346 0.737 1.00 14.23 C \r
+ATOM 4242 CA GLY C 171 0.255 9.724 2.035 1.00 13.78 C \r
+ATOM 4246 CA THR C 172 -0.103 7.560 5.139 1.00 17.62 C \r
+ATOM 4253 CA GLY C 173 3.646 7.343 4.821 1.00 17.20 C \r
+ATOM 4257 CA ILE C 174 3.469 10.213 7.270 1.00 15.91 C \r
+ATOM 4265 CA ALA C 175 2.586 7.783 10.110 1.00 15.63 C \r
+ATOM 4270 CA PRO C 176 6.023 6.933 11.582 1.00 17.04 C \r
+ATOM 4277 CA PHE C 177 7.215 10.514 11.327 1.00 18.21 C \r
+ATOM 4288 CA ARG C 178 4.268 11.745 13.359 1.00 22.35 C \r
+ATOM 4299 CA SER C 179 5.563 9.289 15.983 1.00 25.22 C \r
+ATOM 4305 CA PHE C 180 9.139 10.593 15.614 1.00 25.98 C \r
+ATOM 4316 CA LEU C 181 7.925 14.180 15.767 1.00 29.12 C \r
+ATOM 4324 CA TRP C 182 5.625 13.641 18.714 1.00 31.35 C \r
+ATOM 4338 CA LYS C 183 8.488 12.385 20.871 1.00 30.92 C \r
+ATOM 4347 CA MET C 184 10.841 15.050 19.503 1.00 24.85 C \r
+ATOM 4355 CA PHE C 185 8.741 18.202 20.114 1.00 22.97 C \r
+ATOM 4366 CA PHE C 186 5.604 17.337 22.076 1.00 27.77 C \r
+ATOM 4377 CA GLU C 187 7.117 15.432 25.009 1.00 37.71 C \r
+ATOM 4386 CA LYS C 188 9.542 15.977 27.878 1.00 53.59 C \r
+ATOM 4395 CA HIS C 189 12.355 13.416 28.180 1.00 63.67 C \r
+ATOM 4405 CA ASP C 190 15.318 13.181 30.569 1.00 66.93 C \r
+ATOM 4413 CA ASP C 191 17.480 11.106 28.238 1.00 59.79 C \r
+ATOM 4421 CA TYR C 192 16.190 12.725 25.047 1.00 51.96 C \r
+ATOM 4433 CA LYS C 193 16.700 16.406 24.324 1.00 47.01 C \r
+ATOM 4442 CA PHE C 194 16.580 16.471 20.530 1.00 39.85 C \r
+ATOM 4453 CA ASN C 195 18.572 19.494 19.409 1.00 37.52 C \r
+ATOM 4461 CA GLY C 196 19.361 18.548 15.845 1.00 32.08 C \r
+ATOM 4465 CA LEU C 197 17.310 19.266 12.766 1.00 28.26 C \r
+ATOM 4473 CA GLY C 198 14.051 17.526 11.928 1.00 25.05 C \r
+ATOM 4477 CA TRP C 199 13.211 18.137 8.269 1.00 19.81 C \r
+ATOM 4491 CA LEU C 200 9.908 16.742 7.059 1.00 13.86 C \r
+ATOM 4499 CA PHE C 201 8.855 16.521 3.429 1.00 14.83 C \r
+ATOM 4510 CA LEU C 202 5.288 15.361 2.717 1.00 16.12 C \r
+ATOM 4518 CA GLY C 203 3.701 14.731 -0.681 1.00 13.79 C \r
+ATOM 4522 CA VAL C 204 -0.051 14.414 -1.182 1.00 11.75 C \r
+ATOM 4529 CA PRO C 205 -2.113 15.264 -4.308 1.00 14.66 C \r
+ATOM 4536 CA THR C 206 -4.553 17.737 -2.778 1.00 16.37 C \r
+ATOM 4543 CA SER C 207 -4.756 20.169 0.120 1.00 18.01 C \r
+ATOM 4549 CA SER C 208 -7.780 18.225 1.280 1.00 17.59 C \r
+ATOM 4555 CA SER C 209 -5.452 15.198 1.550 1.00 16.19 C \r
+ATOM 4561 CA LEU C 210 -2.972 16.940 3.860 1.00 14.22 C \r
+ATOM 4569 CA LEU C 211 -2.255 14.980 7.059 1.00 14.43 C \r
+ATOM 4577 CA TYR C 212 -1.624 16.449 10.549 1.00 18.94 C \r
+ATOM 4589 CA LYS C 213 -0.818 19.896 9.150 1.00 22.61 C \r
+ATOM 4598 CA GLU C 214 -2.039 21.572 12.352 1.00 25.73 C \r
+ATOM 4607 CA GLU C 215 0.152 19.413 14.514 1.00 19.23 C \r
+ATOM 4616 CA PHE C 216 3.216 20.178 12.439 1.00 17.80 C \r
+ATOM 4627 CA GLY C 217 2.478 23.890 12.512 1.00 19.90 C \r
+ATOM 4631 CA LYS C 218 2.578 24.001 16.294 1.00 25.54 C \r
+ATOM 4640 CA MET C 219 5.810 22.021 16.188 1.00 26.79 C \r
+ATOM 4648 CA LYS C 220 7.224 24.606 13.819 1.00 31.85 C \r
+ATOM 4657 CA GLU C 221 6.071 27.341 16.219 1.00 38.62 C \r
+ATOM 4666 CA ARG C 222 7.760 25.760 19.233 1.00 39.10 C \r
+ATOM 4677 CA ALA C 223 11.124 24.971 17.668 1.00 35.43 C \r
+ATOM 4682 CA PRO C 224 11.696 27.100 14.528 1.00 32.99 C \r
+ATOM 4689 CA GLU C 225 15.425 26.331 14.360 1.00 33.87 C \r
+ATOM 4698 CA ASN C 226 15.038 22.591 14.986 1.00 30.46 C \r
+ATOM 4706 CA PHE C 227 12.088 21.755 12.732 1.00 24.98 C \r
+ATOM 4717 CA ARG C 228 11.351 22.384 9.075 1.00 19.87 C \r
+ATOM 4728 CA VAL C 229 8.435 21.010 7.118 1.00 14.21 C \r
+ATOM 4735 CA ASP C 230 7.739 21.452 3.398 1.00 12.26 C \r
+ATOM 4743 CA TYR C 231 4.627 20.147 1.722 1.00 14.42 C \r
+ATOM 4755 CA ALA C 232 4.334 19.003 -1.872 1.00 9.99 C \r
+ATOM 4760 CA VAL C 233 0.778 19.232 -3.168 1.00 10.49 C \r
+ATOM 4767 CA SER C 234 1.043 17.769 -6.694 1.00 19.00 C \r
+ATOM 4773 CA ARG C 235 -2.240 19.042 -8.206 1.00 23.13 C \r
+ATOM 4784 CA GLU C 236 -2.069 22.459 -6.578 1.00 17.58 C \r
+ATOM 4793 CA GLN C 237 1.546 23.511 -6.623 1.00 15.89 C \r
+ATOM 4802 CA THR C 238 4.202 24.018 -9.275 1.00 17.86 C \r
+ATOM 4809 CA ASN C 239 7.922 24.800 -9.182 1.00 15.15 C \r
+ATOM 4817 CA ALA C 240 9.558 27.791 -10.892 1.00 21.51 C \r
+ATOM 4822 CA ALA C 241 9.475 25.887 -14.174 1.00 24.05 C \r
+ATOM 4827 CA GLY C 242 5.741 25.110 -13.938 1.00 26.25 C \r
+ATOM 4831 CA GLU C 243 5.999 21.359 -13.153 1.00 25.92 C \r
+ATOM 4840 CA ARG C 244 3.679 19.536 -10.704 1.00 24.04 C \r
+ATOM 4851 CA MET C 245 5.076 19.643 -7.174 1.00 18.58 C \r
+ATOM 4859 CA TYR C 246 5.784 16.047 -6.100 1.00 14.16 C \r
+ATOM 4871 CA ILE C 247 7.910 15.343 -3.034 1.00 16.78 C \r
+ATOM 4879 CA GLN C 248 11.089 15.070 -5.120 1.00 18.72 C \r
+ATOM 4888 CA THR C 249 10.168 18.255 -6.921 1.00 20.93 C \r
+ATOM 4895 CA ARG C 250 9.962 20.031 -3.567 1.00 19.25 C \r
+ATOM 4906 CA MET C 251 13.275 18.471 -2.561 1.00 19.40 C \r
+ATOM 4914 CA ALA C 252 14.910 19.812 -5.760 1.00 20.48 C \r
+ATOM 4919 CA GLU C 253 14.456 23.418 -4.569 1.00 18.19 C \r
+ATOM 4928 CA TYR C 254 16.804 22.515 -1.673 1.00 17.80 C \r
+ATOM 4940 CA LYS C 255 19.038 20.415 -3.902 1.00 20.66 C \r
+ATOM 4949 CA GLU C 256 22.452 21.603 -2.682 1.00 16.05 C \r
+ATOM 4958 CA GLU C 257 21.544 21.914 0.993 1.00 15.89 C \r
+ATOM 4967 CA LEU C 258 20.377 18.297 0.919 1.00 20.74 C \r
+ATOM 4975 CA TRP C 259 23.388 16.939 -0.965 1.00 23.45 C \r
+ATOM 4989 CA GLU C 260 25.645 18.669 1.563 1.00 24.08 C \r
+ATOM 4998 CA LEU C 261 23.573 17.378 4.477 1.00 24.74 C \r
+ATOM 5006 CA LEU C 262 24.020 13.928 2.938 1.00 26.14 C \r
+ATOM 5014 CA LYS C 263 27.792 14.091 3.402 1.00 25.40 C \r
+ATOM 5023 CA LYS C 264 27.457 14.521 7.176 1.00 31.47 C \r
+ATOM 5032 CA ASP C 265 27.877 11.474 9.425 1.00 35.31 C \r
+ATOM 5040 CA ASN C 266 24.934 12.482 11.620 1.00 29.63 C \r
+ATOM 5048 CA THR C 267 22.321 12.795 8.832 1.00 28.00 C \r
+ATOM 5055 CA TYR C 268 19.556 10.160 8.808 1.00 27.00 C \r
+ATOM 5067 CA VAL C 269 17.143 9.903 5.884 1.00 24.65 C \r
+ATOM 5074 CA TYR C 270 13.890 8.016 6.276 1.00 23.37 C \r
+ATOM 5086 CA MET C 271 11.373 7.327 3.518 1.00 18.93 C \r
+ATOM 5094 CA CYS C 272 7.834 6.074 4.043 1.00 18.24 C \r
+ATOM 5100 CA GLY C 273 4.784 5.874 1.826 1.00 22.39 C \r
+ATOM 5104 CA LEU C 274 3.837 4.483 -1.568 1.00 26.95 C \r
+ATOM 5112 CA LYS C 275 6.305 2.384 -3.532 1.00 32.36 C \r
+ATOM 5121 CA GLY C 276 7.741 4.199 -6.514 1.00 37.46 C \r
+ATOM 5125 CA MET C 277 7.714 7.455 -4.608 1.00 28.76 C \r
+ATOM 5133 CA GLU C 278 11.430 6.639 -4.425 1.00 32.22 C \r
+ATOM 5142 CA LYS C 279 12.017 6.321 -8.153 1.00 29.94 C \r
+ATOM 5151 CA GLY C 280 11.317 10.057 -8.293 1.00 24.18 C \r
+ATOM 5155 CA ILE C 281 13.766 10.673 -5.460 1.00 23.68 C \r
+ATOM 5163 CA ASP C 282 16.431 8.365 -6.934 1.00 26.58 C \r
+ATOM 5171 CA ASP C 283 16.211 10.530 -10.054 1.00 28.70 C \r
+ATOM 5179 CA ILE C 284 17.089 13.937 -8.538 1.00 27.28 C \r
+ATOM 5187 CA MET C 285 19.706 12.222 -6.388 1.00 27.45 C \r
+ATOM 5195 CA VAL C 286 21.377 10.712 -9.470 1.00 30.74 C \r
+ATOM 5202 CA SER C 287 21.619 14.159 -11.061 1.00 32.14 C \r
+ATOM 5208 CA LEU C 288 23.240 15.463 -7.873 1.00 34.20 C \r
+ATOM 5216 CA ALA C 289 25.801 12.653 -7.874 1.00 40.16 C \r
+ATOM 5221 CA GLU C 290 26.837 12.825 -11.536 1.00 41.84 C \r
+ATOM 5230 CA LYS C 291 27.855 16.387 -10.793 1.00 43.17 C \r
+ATOM 5239 CA ASP C 292 30.299 15.115 -8.139 1.00 41.84 C \r
+ATOM 5247 CA GLY C 293 31.237 12.232 -10.420 1.00 46.12 C \r
+ATOM 5251 CA ILE C 294 30.053 9.669 -7.864 1.00 45.54 C \r
+ATOM 5259 CA ASP C 295 27.399 6.998 -8.480 1.00 41.14 C \r
+ATOM 5267 CA TRP C 296 24.222 7.605 -6.479 1.00 30.67 C \r
+ATOM 5281 CA PHE C 297 23.381 3.910 -6.151 1.00 31.97 C \r
+ATOM 5292 CA ASP C 298 26.856 2.916 -4.907 1.00 38.12 C \r
+ATOM 5300 CA TYR C 299 26.671 5.875 -2.540 1.00 39.05 C \r
+ATOM 5312 CA LYS C 300 23.196 4.971 -1.294 1.00 41.63 C \r
+ATOM 5321 CA LYS C 301 24.542 1.489 -0.577 1.00 43.40 C \r
+ATOM 5330 CA GLN C 302 27.207 3.064 1.608 1.00 43.79 C \r
+ATOM 5339 CA LEU C 303 24.476 5.181 3.238 1.00 41.51 C \r
+ATOM 5347 CA LYS C 304 22.138 2.343 4.264 1.00 45.18 C \r
+ATOM 5356 CA ARG C 305 25.322 0.535 5.256 1.00 46.65 C \r
+ATOM 5367 CA GLY C 306 25.613 3.181 7.945 1.00 40.29 C \r
+ATOM 5371 CA ASP C 307 21.954 3.487 8.940 1.00 41.21 C \r
+ATOM 5379 CA GLN C 308 21.463 6.730 7.023 1.00 35.55 C \r
+ATOM 5388 CA TRP C 309 18.961 5.674 4.361 1.00 31.22 C \r
+ATOM 5402 CA ASN C 310 16.018 3.728 5.752 1.00 31.61 C \r
+ATOM 5410 CA VAL C 311 13.120 2.841 3.452 1.00 32.13 C \r
+ATOM 5417 CA GLU C 312 9.705 1.332 4.261 1.00 31.51 C \r
+ATOM 5426 CA VAL C 313 7.466 1.606 1.209 1.00 26.39 C \r
+ATOM 5433 CA TYR C 314 4.403 -0.343 0.111 1.00 25.42 C \r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r<head>\r<!-- InstanceBeginEditable name="doctitle" -->
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+ <p><strong>Download the applet jar file from <a
+ href="jalviewApplet.jar">here</a>. Parameters are described
+ <a href="#parameters">below</a>, and the javascript API is described <a href="formComplete.html">here</a></strong>.
+ </p>
+ <h3 align="left">Useful to know!!</h3>
+ <ul>
+ <li>Package all your data files into a single (or multiple) zip / jar
+ files. This is very useful to reduce download time of large data files.
+ The applet archive tag can take multiple entries separated by commas,
+ eg<br>
+ <font face="Courier New, Courier, mono" align="left"><applet code="jalview.bin.JalviewLite"<em><strong>
+ archive="jalviewApplet.jar, mydata.zip"</strong></em>><br>
+ </font></li>
+ <li> Use Jalview for input to a HTML form. For an example of how to
+ code this using Javascript, click <a href="formComplete.html">here</a>.
+ <br>
+ </li>
+ <li>Embed Jalview into the web page, without the "Start Jalview"
+ button by setting the embed parameter to true;<br>
+ <param name="embedded"
+ value="true"> </li>
+ </ul>
\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>
\r <ul>
\r <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series - <a href="JmolApplet-12.1.13.jar">download the JmolApplet here</a></font></li>
\r<li>To use Jmol as the structure viewer for Jalview, you must include
\r the jar file in the applet archive argument thus:<br>
\r <pre><font size="2">archive="jalviewApplet.jar,Jmol-12.1.13.jar"</font></pre>
\r </li>
\r <li>Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have
\r Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the
\r original Jalview structure viewer will still be available. <br>
\r </li>
\r <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from
\r the Jmol binary distribution available at the Jmol Sourceforge site,
\r or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
\r <li><font size="2">Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</font></li>
\r </ul>
+ <br><strong><font size="2">**NEW FEATURES** in Jalview 2.5</font></strong></p>
\r <ul>
\r <li><font size="2">New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</font></li>
\r </ul>
\r <br><strong><font size="2">**NEW FEATURES** in Jalview 2.4</font></strong></p>
+ <ul>
+ <li><font size="2">New applet API methods for feature display control, views, and obtaining current selection via javascript.</font></li>
+ <li><font size="2">Group show and hide parameters:
+ "showfeaturegroups" and
+ "hidefeaturegroups". Both take a list
+ of feature group names (separarated by "|" by default) to hide or show on the displayed
+ alignment.</font>
+ </li>
+ <li><font size="2">Regular expressions can be used in URL links for sequence IDs.</font></li>
+ <li><font size="2">"debug" parameter to control verbosity of the applet's console output.</font></li>
+ <li><font size="2">"showbutton" parameter to disable launch button and open JalviewLite immediatly.</font></li>
+ <li><font size="2">"nojmol" parameter to disable check for Jmol classes.</font></li>
+ </ul><br>
+ <strong><font size="2">**NEW FEATURES** in Jalview 2.3</font></strong></p>
+ <ul>
+ <li><font size="2">Note that Parameter "PDBFile" now takes
+ the PDB file followed by a space separated list of alignment sequence
+ ids to associate the structure to. It is also possible to associate
+ multiple PDB files by adding an incremental value to PDBFile (up to
+ 10). It is also possible to map specific sequences to specific chains
+ by using the following notation:<br>
+ <br>
+ <param name="PDBFile" value="First.pdb SeqA SeqB
+ SeqC"> </font><br>
+ <font size="2"><param name="PDBFile2" value="Second.pdb
+ A=SeqA B=SeqB C=SeqC"> </font><br>
+ <font size="2"><param name="PDBFile3" value="Third.pdb
+ D=SeqX B=SeqY C=SeqZ"> </font> <br>
+ </li>
+ <li>Note parameter "PDBSeq" is no longer required.<br>
+ </li>
+ <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="../versions.html">versions archive if you want to download the old Jmol applet</a>.</li>
+ <p> </p>
+ </li>
+ </ul>
+ <strong><font size="2">**NEW FEATURES** in Jalview 2.1</font></strong>
+ <ul>
+ <li>Jalview Applet can read and display JNet secondary structure annotation
+ directly via the <strong>jnetfile</strong> parameter. <br>
+ </li>
+ <li>Param <font face="Courier New, Courier, mono">UserDefinedColour</font><em>
+ </em>- specify your own colours for each residue using a semi colon
+ separated list. Multiple residues can be assigned the same colour
+ using commas. eg:<br>
+ <font face="Courier New, Courier, mono"><param name="userDefinedColour"
+ value="D,E=red; K,R,H=0022FF; C=yellow"></font><br>
+ </li>
+ <li>Param <font face="Courier New, Courier, mono">showFeatureSettings</font>
+ - this will display the feature settings window when the applet starts.<br>
+ </li>
+ <li>Param <font face="Courier New, Courier, mono">Application_URL value="http://www.jalview.org/services/launchApp"<br>
+ </font>This calls a servlet which creates a JNLP file with the alignment
+ file, annotations file and features file of the applet as arguments.
+ If the user has Java installed, the returned JNLP file should start
+ up the full Jalview Application. BUT this does not currently work
+ for alignment files added to the applet in a zip file.<br>
+ </li>
+ <li>Alignment file can be a series of parameters using eg PFAM format
+ <br>
+ <font face="Courier New, Courier, mono"><param name="sequence1"
+ value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI"><br>
+ <param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT"><br>
+ </font>(All the usual Jalview File formats are valid, however each
+ new line in an alignment file must be entered as a parameter)<font face="Courier New, Courier, mono"><br>
+ </font> </li>
+ </ul>
+ <a name="parameters"></a> <table width="97%" border="1" align="center" >
+ <tr>
+ <td width="103" height="23"><strong><param name=""</strong></td>
+ <td width="80" ><strong>value=""></strong></td>
+ <td width="100%"><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td>file</td>
+ <td>fileName</td>
+ <td>The file to open, must be on same server as the applet.</td>
+ </tr>
+ <tr>
+ <td>sequence1,<br>
+ sequence2,<br>
+ sequence3</td>
+ <td>sequence in (preferably) PFAM or Fasta format</td>
+ <td>The alignment can be added as a series of sequences instead of
+ from a file.</td>
+ </tr>
+ <tr>
+ <td>tree</td>
+ <td>fileName</td>
+ <td>Tree file in Newick format</td>
+ </tr>
+ <tr>
+ <td>features</td>
+ <td>fileName</td>
+ <td>Jalview Features file to be applied to the alignment</td>
+ </tr>
+ <tr>
+ <td>annotations</td>
+ <td>fileName</td>
+ <td>Jalview Annotation file will be added to the alignment</td>
+ </tr>
+ <tr>
+ <td>jnetfile</td>
+ <td>fileName</td>
+ <td>Secondary structure predictions from a <a
+ href="http://www.compbio.dundee.ac.uk/~www-jpred/">Jnet</a> Concise
+ file will be added to the first sequence in the alignment.</td>
+ </tr>
+ <tr>
+ <td>PDBfile(x)</td>
+ <td><p>fileName seq1 seq2 seq3</p>
+ <p>or</p>
+ <p>fileName A=seq1 B=seq2 C=seq3</p></td>
+ <td>PDB file which is to be associated with a sequence, followed by
+ space separated list of alignment sequence ids. PDB chains can be
+ specifed to map to particular sequence by using A=SeqA notation</td>
+ </tr>
+ <tr>
+ <td><p>PDBSeq<br>
+ *Not needed post Jalview 2.3, use PDBFile instead</p></td>
+ <td>SequenceId</td>
+ <td>The sequence to associate a PDB file with. Note the value is case
+ sensitive.</td>
+ </tr>
+ <tr>
+ <td>defaultColour</td>
+ <td> <em>One of: </em><br>
+ Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide</td>
+ <td>Default is no colour.</td>
+ </tr>
+ <tr>
+ <td>userDefinedColour</td>
+ <td><p><em>Example:</em><br>
+ D,E=red; K,R,H=0022FF; c=yellow</p></td>
+ <td>Define residue colours</td>
+ </tr>
+ <tr>
+ <td height="35">showFullId</td>
+ <td>true <em>or</em> false</td>
+ <td>if true displays start and end residue at the end of sequence
+ Id.</td>
+ </tr>
+ <tr>
+ <td>showAnnotation</td>
+ <td>true <em>or</em> false</td>
+ <td>If true shows the annotation panel below the alignment.</td>
+ </tr>
+ <tr>
+ <td>showConservation</td>
+ <td>true <em>or</em> false</td>
+ <td>Default is true.</td>
+ </tr>
+ <tr>
+ <td>showQuality</td>
+ <td>true <em>or</em> false</td>
+ <td>Default is true.</td>
+ </tr>
+ <tr>
+ <td>showConsensus</td>
+ <td>true <em>or</em> false</td>
+ <td>Default is true.</td>
+ </tr>
+ <tr>
+ <td>sortBy</td>
+ <td> Id <em>, </em> Pairwise Identity<em>, or</em> Length</td>
+ <td> Sorts the alignment on startup</td>
+ </tr>
+ <tr>
+ <td>RGB</td>
+ <td>colour as hex string</td>
+ <td>Background colour for applet button - purely cosmetic to blend
+ in with your web page. For orange, enter the value FF6600</td>
+ </tr>
+ <tr>
+ <td>embedded</td>
+ <td>true <em>or</em> false</td>
+ <td>The applet is embedded in the web page, the "Start Jalview"
+ button is not displayed.</td>
+ </tr>
+ <tr>
+ <td>windowWidth</td>
+ <td>value</td>
+ <td>frame width</td>
+ </tr>
+ <tr>
+ <td>windowHeight</td>
+ <td>value</td>
+ <td>frame height</td>
+ </tr>
+ <tr>
+ <td>label</td>
+ <td>label text</td>
+ <td>Change text for the Launch Jalview Button</td>
+ </tr>
+ <tr>
+ <td>wrap</td>
+ <td>true <em>or</em> false</td>
+ <td>Opens new windows in wrapped mode</td>
+ </tr>
+ <tr>
+ <td>linkLabel_1</td>
+ <td>Uniprot</td>
+ <td rowspan="2"><p>Right click on sequence id to see list of available
+ links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n
+ value. For multiple links, increment the label and url name by
+ 1. ie <br>
+ <param name="linkLabel_2" ..., <br>
+ <param name="linkUrl_2"....<br>
+ </p>
+ <p>Regular expressions may also be used (<em>since Jalview 2.4</em>) to process the ID string inserted into the URL:
+ <br>$SEQUENCE_ID=/<regex to extract ID>/=$<br><em>Use the debug flag to check parsing and make sure that special symbols are properly escaped (particularly when generating applet tags from CGI scripts).
+ <br>Regex URL links are also applied to the description line (since Jalview 2.4.+).</em></p></td>
+ </tr>
+ <tr>
+ <td> <p><br>
+ linkUrl_1<br>
+ </p></td>
+ <td><p><br>
+ http://us.expasy.org/cgi-bin/<br>
+ niceprot.pl?$SEQUENCE_ID$</p>
+ </td>
+ </tr>
+ <tr>
+ <td>showFeatureSettings</td>
+ <td>true <em>or</em> false</td>
+ <td>Shows the feature settings window when starting the applet</td>
+ </tr>
+ <tr>
+ <td>showfeaturegroups</td>
+ <td><em>separator</em> separated list of feature groups</td>
+ <td>Display the features in the given groups on the alignment</td>
+ </tr>
+ <tr>
+ <td>hidefeaturegroups</td>
+ <td><em>separator</em> separated list of feature groups</td>
+ <td>Hide the features in the given groups on the alignment
+ (will be overridden by showfeaturegroups for group names
+ found in both lists)</td>
+ </tr>
+ <tr>
+ <td>application_url</td>
+ <td><p><em>URL of dynamic JNLP servlet,</em></p>
+ <p>http://www.jalview.org/services/launchApp</p></td>
+ <td>Launches full application with original alignment, features and
+ annotations files used in applet</td>
+ </tr>
+ <tr>
+ <td>separator</td>
+ <td><em>non-empty separator string</em><br>default: |</td>
+ <td>string used to separate fields in list parameters (such as <em>showfeaturegroups</em>)</td>
+ </tr>
+ <tr><td>debug</td>
+ <td>true</td>
+ <td>Instruct the applet to output additional debug messages to the java console</td>
+ </tr>
+ <tr><td>nojmol</td>
+ <td>false</td>
+ <td>When set, do not try to find Jmol classes. Set this to supress URL not found errors appearing
+ in server logs when Jmol is not available.
+ </td>
+ </tr>
+ <tr><td>showbutton</td>
+ <td>true</td>
+ <td>Show the jalview button on the page. When false, JalviewLite will open immediately.</td>
+ </tr>\r </tr>\r <tr><td>sortByTree</td>\r <td>true or false (default is false)</td>\r <td>automatically sort the associated alignment view by the tree when a new tree is opened.</td>\r </tr>\r <tr>\r <td>showTreeBootstraps</td><td>true or false (default is true)</td><td>show or hide branch bootstraps</td>\r </tr>\r <tr><td>showTreeDistances</td><td>true or false (default is true)</td><td>show or hide branch lengths</td></tr>\r <tr><td>showUnlinkedTreeNodes</td><td>true or false (default is false)</td><td>indicate if unassociated nodes should be highlighted in the tree view</td>\r </tr>\r <tr><td>heightScale</td>\r <td>1.0 or greater</td>\r <td>Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font.</td>\r </tr>
+ <tr><td>widthScale</td>\r <td>1.0 or greater</td>\r <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font.</td>\r </tr>\r </table>
+ <p align="center"> </p>
+ <!-- InstanceEndEditable --></td>\r </tr>\r </table>\r</div>\r</body>\r<!-- InstanceEnd --></html>\r
\ No newline at end of file
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r<head>\r<!-- InstanceBeginEditable name="doctitle" -->
+<TITLE>Jalview - Applets</TITLE>
+<!-- InstanceEndEditable -->
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\r <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
\r Version</a></td>
\r </tr>
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\r <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
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\r Code</a></td>
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\r <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
+ <p>Jalview comes in two distinct flavours.<br>
+ <br>
+ The main application allows connection to multiple web services provided
+ at the University of Dundee as well as a host of additional useful features
+ such as printing, making images from your alignment and annotating your
+ alignment. You need to download and install this software.</p>
+ <p>The applet version runs in web browsers and is a useful interactive
+ display for precalculated alignments, features and annotations files.
+ It does not have the full functionality of the main application, such
+ as making images, saving files, running web service jobs due to security
+ restrictions imposed on applets.</p>
+ <p align="left">For more information on how to use the applet in your
+ website, see <a href="appletParameters.html"><strong>full list of applet
+ parameters.</strong></a></p>
+ <p> Pressing one of the buttons below will load up a cut down version
+ of Jalview, which runs within your web browser. </p>
+ <H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
+ cluster<br>
+ (15 sequences x 150 residues)</H4>
+ <div align="center"> </div>
+ <div align="center">
+ <table width="300" border="1" cellspacing="0" cellpadding="0">
+ <tr>
+ <td><table width="300" border="0" cellspacing="0" cellpadding="0">
+ <tr>
+ <td width="100"> <applet code="jalview.bin.JalviewLite"
+ width="140" height="35"
+ archive="jalviewApplet.jar">
+ <param name="file" value="uniref50.fa">
+ <param name="treeFile" value="ferredoxin.nw">
+ <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF">
+ <param name="showFullId" value="false">
+ <param name="RGB" value="F2F2FF">
+ <param name="linkLabel_1" value="SRS">
+ <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
+ <param name="linkLabel_2" value="Uniprot">
+ <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
+ </applet></td>
+ <td width="165">User Defined Colours, loads an associated Newick
+ format tree file</td>
+ </tr>
+ </table></td>
+ </tr>
+ </table>
+ <p> </p>
+ <table width="300" border="1" cellspacing="0" cellpadding="0">
+ <tr>
+ <td><table width="300" border="0" cellspacing="0" cellpadding="0">
+ <tr>
+ <td width="100"> <applet code="jalview.bin.JalviewLite"
+ width="140" height="35"
+ archive="jalviewApplet.jar">
+ <param name="file" value="uniref50.fa">
+ <param name="features" value="exampleFeatures.txt">
+ <param name="showFeatureSettings" value="true">
+ <param name="wrap" value="true">
+ <param name="showAnnotation" value="false">
+ <param name="windowHeight" value="500">
+ <param name="windowWidth" value="650">
+ <param name="showFullId" value="false">
+ <param name="RGB" value="F2F2FF">
+ <param name="linkLabel_1" value="SRS">
+ <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
+ <param name="linkLabel_2" value="Uniprot">
+ <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
+ </applet> </td>
+ <td width="165">Displays a features file on the alignment</td>
+ </tr>
+ </table></td>
+ </tr>
+ </table>
+ <p> </p>
+ <table width="300" border="1" cellspacing="0" cellpadding="0">
+ <tr>
+ <td><table width="300" border="0" cellspacing="0" cellpadding="0">
+ <tr>
+ <td width="100"> <applet code="jalview.bin.JalviewLite"
+ width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-12.1.13.jar">
+ <param name="file" value="uniref50.fa">
+ <param name="defaultColour" value="Strand Propensity">
+ <param name="wrap" value="true">
+ <param name="showAnnotation" value="false">
+ <param name="windowHeight" value="500">
+ <param name="windowWidth" value="650">
+ <param name="showFullId" value="false">
+ <param name="RGB" value="F2F2FF">
+ <param name="linkLabel_1" value="SRS">
+ <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
+ <param name="linkLabel_2" value="Uniprot">
+ <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
+ <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
+ </applet> </td>
+ <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
+ </tr>
+ </table></td>
+ </tr>
+ </table>
+ <p> </p>
+ <table width="300" border="1" cellspacing="0" cellpadding="0">
+ <tr>
+ <td><table width="300" border="0" cellspacing="0" cellpadding="0">
+ <tr>
+ <td width="100"> <applet code="jalview.bin.JalviewLite"
+ width="140" height="35"
+ archive="jalviewApplet.jar">
+ <param name="file" value="jpred_msa.fasta">
+ <param name="jnetfile" value="jpred_msa.seq.concise">
+ <param name="defaultColour" value="Clustal">
+ <param name="showAnnotation" value="true">
+ <param name="windowHeight" value="515">
+ <param name="windowWidth" value="650">
+ <param name="showConservation" value="false">
+ <param name="showQuality" value="false">
+ <param name="showConsensus" value="false">
+ <param name="showFullId" value="false">
+ <param name="RGB" value="F2F2FF">
+ <param name="linkLabel_1" value="SRS">
+ <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
+ <param name="linkLabel_2" value="Uniprot">
+ <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
+ </applet> </td>
+ <td width="165">Displays a Multiple Sequence Alignment Based
+ JNet Prediction for a Sequence</td>
+ </tr>
+ </table></td>
+ </tr>
+ </table>
+ </div>
+ <!-- InstanceEndEditable --></td>\r </tr>\r </table>\r</div>\r</body>\r<!-- InstanceEnd --></html>\r
\ No newline at end of file
--- /dev/null
+ST-TURN-IIL 705b23\r
+GAMMA-TURN-CLASSIC 788763\r
+BETA-TURN-IR 9a6a94\r
+BETA-TURN-IL d6a6ca\r
+BETA-BULGE 1dc451\r
+Pfam dc206a\r
+PHOSPHORYLATION (S) b974a5\r
+PHOSPHORYLATION (Y) 7d3881\r
+Cath 93b1d2\r
+ASX-TURN-IR 4ccc6e\r
+BETA-BULGE-LOOP-5 4066da\r
+CATMAT-4 4dc465\r
+CATMAT-3 3eb555\r
+GAMMA-TURN-INVERSE 7881c7\r
+SCHELLMANN-LOOP-6 a28bbb\r
+METAL cc9900\r
+ALPHA-BETA-MOTIF 7bd649\r
+ASX-MOTIF 6addbb\r
+NEST-LR 3e16d0\r
+ASX-TURN-IIR 6a4062\r
+NEST-RL 3e16b2\r
+ASX-TURN-IIL a67c98\r
+BETA-TURN-IIR c79792\r
+PHOSPHORYLATION (T) c88395\r
+BETA-TURN-IIL 8b5b50\r
+ST-MOTIF ac25a1\r
+\r
+STARTGROUP uniprot\r
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL\r
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL\r
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL\r
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 8_8</a></html> FER_CAPAA -1 8 83 Pfam\r
+Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath\r
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL\r
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL\r
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL\r
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 55_13</a></html> FER_CAPAN -1 55 130 Pfam\r
+Ferredoxin_fold Status: True Positive FER_CAPAN -1 45 140 Cath\r
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL\r
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL\r
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL\r
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 55_13</a></html> FER1_SOLLC -1 55 130 Pfam\r
+Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 55_13</a></html> Q93XJ9_SOLTU -1 55 130 Pfam\r
+Ferredoxin_fold Status: True Positive Q93XJ9_SOLTU -1 45 140 Cath\r
+Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL\r
+Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL\r
+Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL\r
+Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 60_13</a></html> FER1_PEA -1 60 135 Pfam\r
+Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 63_13</a></html> Q7XA98_TRIPR -1 63 138 Pfam\r
+Ferredoxin_fold Status: True Positive Q7XA98_TRIPR -1 53 148 Cath\r
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL\r
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL\r
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL\r
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 59_13</a></html> FER1_MESCR -1 59 134 Pfam\r
+Ferredoxin_fold Status: True Positive FER1_MESCR -1 49 144 Cath\r
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL\r
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL\r
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL\r
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 58_13</a></html> FER1_SPIOL -1 58 133 Pfam\r
+Ferredoxin_fold Status: True Positive FER1_SPIOL -1 48 143 Cath\r
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL\r
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL\r
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL\r
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 8_8</a></html> FER3_RAPSA -1 8 83 Pfam\r
+Ferredoxin_fold Status: True Positive FER3_RAPSA -1 3 93 Cath\r
+Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL\r
+Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL\r
+Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL\r
+Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 8_8</a></html> FER_BRANA -1 8 83 Pfam\r
+Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath\r
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL\r
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL\r
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL\r
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 60_13</a></html> FER2_ARATH -1 60 135 Pfam\r
+Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 60_11</a></html> Q93Z60_ARATH -1 60 118 Pfam\r
+Ferredoxin_fold Status: True Positive Q93Z60_ARATH -1 52 118 Cath\r
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL\r
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL\r
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL\r
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 60_13</a></html> FER1_MAIZE -1 60 135 Pfam\r
+Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath\r
+<html>Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 52_12</a></html> O80429_MAIZE -1 52 127 Pfam\r
+Ferredoxin_fold Status: True Positive O80429_MAIZE -1 42 137 Cath\r
+ENDGROUP uniprot\r
+\r
+\r
+STARTGROUP netphos\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html> FER_CAPAA -1 89 89 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (S) 22_2</a></html> FER1_SOLLC -1 22 22 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html> FER1_SOLLC -1 38 38 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (S) 102_10</a></html> FER1_SOLLC -1 102 102 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q43517&service=NetPhos-2.0">PHOSPHORYLATION (T) 136_13</a></html> FER1_SOLLC -1 136 136 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&service=NetPhos-2.0">PHOSPHORYLATION (T) 136_13</a></html> Q93XJ9_SOLTU -1 136 136 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&service=NetPhos-2.0">PHOSPHORYLATION (S) 22_2</a></html> Q93XJ9_SOLTU -1 22 22 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93XJ9&service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html> Q93XJ9_SOLTU -1 38 38 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 33_3</a></html> FER1_PEA -1 33 33 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 42_4</a></html> FER1_PEA -1 42 42 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html> FER1_PEA -1 90 90 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_PEA -1 114 114 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (T) 4_</a></html> FER1_PEA -1 4 4 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (T) 28_2</a></html> FER1_PEA -1 28 28 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P09911&service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_PEA -1 141 141 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (S) 117_11</a></html> Q7XA98_TRIPR -1 117 117 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 137_13</a></html> Q7XA98_TRIPR -1 137 137 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 144_14</a></html> Q7XA98_TRIPR -1 144 144 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 30_3</a></html> Q7XA98_TRIPR -1 30 30 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 31_3</a></html> Q7XA98_TRIPR -1 31 31 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 4_</a></html> Q7XA98_TRIPR -1 4 4 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (S) 45_4</a></html> Q7XA98_TRIPR -1 45 45 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (T) 46_4</a></html> Q7XA98_TRIPR -1 46 46 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q7XA98&service=NetPhos-2.0">PHOSPHORYLATION (S) 93_9</a></html> Q7XA98_TRIPR -1 93 93 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (S) 88_8</a></html> FER1_SPIOL -1 88 88 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (S) 112_11</a></html> FER1_SPIOL -1 112 112 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (T) 139_13</a></html> FER1_SPIOL -1 139 139 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&service=NetPhos-2.0">PHOSPHORYLATION (Y) 73_7</a></html> FER1_SPIOL -1 73 73 PHOSPHORYLATION (Y)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html> FER1_ARATH -1 19 19 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html> FER1_ARATH -1 24 24 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html> FER1_ARATH -1 90 90 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER1_ARATH -1 107 107 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_ARATH -1 114 114 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_ARATH -1 141 141 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html> FER1_ARATH -1 75 75 PHOSPHORYLATION (Y)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html> FER_BRANA -1 38 38 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (S) 62_6</a></html> FER_BRANA -1 62 62 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html> FER_BRANA -1 89 89 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&service=NetPhos-2.0">PHOSPHORYLATION (Y) 23_2</a></html> FER_BRANA -1 23 23 PHOSPHORYLATION (Y)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> Q93Z60_ARATH -1 107 107 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> Q93Z60_ARATH -1 114 114 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (T) 21_2</a></html> Q93Z60_ARATH -1 21 21 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html> Q93Z60_ARATH -1 24 24 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=Q93Z60&service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html> Q93Z60_ARATH -1 75 75 PHOSPHORYLATION (Y)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 7_</a></html> FER1_MAIZE -1 7 7 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html> FER1_MAIZE -1 19 19 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 44_4</a></html> FER1_MAIZE -1 44 44 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 45_4</a></html> FER1_MAIZE -1 45 45 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html> FER1_MAIZE -1 90 90 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER1_MAIZE -1 107 107 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_MAIZE -1 114 114 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (T) 134_13</a></html> FER1_MAIZE -1 134 134 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_MAIZE -1 141 141 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P27787&service=NetPhos-2.0">PHOSPHORYLATION (Y) 115_11</a></html> FER1_MAIZE -1 115 115 PHOSPHORYLATION (Y)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (T) 133_13</a></html> O80429_MAIZE -1 133 133 PHOSPHORYLATION (T)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (S) 82_8</a></html> O80429_MAIZE -1 82 82 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (S) 9_</a></html> O80429_MAIZE -1 9 9 PHOSPHORYLATION (S)\r
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=O80429&service=NetPhos-2.0">PHOSPHORYLATION (S) 99_9</a></html> O80429_MAIZE -1 99 99 PHOSPHORYLATION (S)\r
+ENDGROUP netphos\r
+\r
+STARTGROUP s3dm\r
+<html>Found in PDBs: 1a70.,1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 115_11</a></html> FER1_SPIOL -1 115 119 ALPHA-BETA-MOTIF\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/asxturniil?gzip=false">ASX-TURN-IIL 107_10</a></html> FER1_SPIOL -1 107 109 ASX-TURN-IIL\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/asxturnir?gzip=false">ASX-TURN-IR 115_11</a></html> FER1_SPIOL -1 115 117 ASX-TURN-IR\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betabulge?gzip=false">BETA-BULGE 102_10</a></html> FER1_SPIOL -1 102 103 BETA-BULGE\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 59_6</a></html> FER1_SPIOL -1 59 62 BETA-TURN-IR\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 69_7</a></html> FER1_SPIOL -1 69 72 BETA-TURN-IR\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 95_9</a></html> FER1_SPIOL -1 95 98 BETA-TURN-IR\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 108_11</a></html> FER1_SPIOL -1 108 111 BETA-TURN-IR\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 125_12</a></html> FER1_SPIOL -1 125 128 BETA-TURN-IR\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 141_14</a></html> FER1_SPIOL -1 141 144 BETA-TURN-IR\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 90_9</a></html> FER1_SPIOL -1 90 92 NEST-LR\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 92_9</a></html> FER1_SPIOL -1 92 94 NEST-LR\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 140_14</a></html> FER1_SPIOL -1 140 142 NEST-LR\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 81_8</a></html> FER1_SPIOL -1 81 83 NEST-RL\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 89_9</a></html> FER1_SPIOL -1 89 91 NEST-RL\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 91_9</a></html> FER1_SPIOL -1 91 93 NEST-RL\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 121_12</a></html> FER1_SPIOL -1 121 123 NEST-RL\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/schellmannloop6?gzip=false">SCHELLMANN-LOOP-6 78_8</a></html> FER1_SPIOL -1 78 83 SCHELLMANN-LOOP-6\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/schellmannloop6?gzip=false">SCHELLMANN-LOOP-6 118_12</a></html> FER1_SPIOL -1 118 123 SCHELLMANN-LOOP-6\r
+<html>Found in PDBs: 1a70. <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/stmotif?gzip=false">ST-MOTIF 59_6</a></html> FER1_SPIOL -1 59 63 ST-MOTIF\r
+ALPHA-BETA-MOTIF FER1_SPIOL -1 65 69 ALPHA-BETA-MOTIF\r
+ASX-MOTIF FER1_SPIOL -1 65 69 ASX-MOTIF\r
+ASX-TURN-IIL FER1_SPIOL -1 57 59 ASX-TURN-IIL\r
+ASX-TURN-IR FER1_SPIOL -1 65 67 ASX-TURN-IR\r
+BETA-BULGE FER1_SPIOL -1 52 53 BETA-BULGE\r
+BETA-TURN-IR FER1_SPIOL -1 9 12 BETA-TURN-IR\r
+BETA-TURN-IR FER1_SPIOL -1 19 22 BETA-TURN-IR\r
+BETA-TURN-IR FER1_SPIOL -1 45 48 BETA-TURN-IR\r
+BETA-TURN-IR FER1_SPIOL -1 58 61 BETA-TURN-IR\r
+BETA-TURN-IR FER1_SPIOL -1 75 78 BETA-TURN-IR\r
+BETA-TURN-IR FER1_SPIOL -1 91 94 BETA-TURN-IR\r
+NEST-LR FER1_SPIOL -1 40 42 NEST-LR\r
+NEST-LR FER1_SPIOL -1 42 44 NEST-LR\r
+NEST-LR FER1_SPIOL -1 90 92 NEST-LR\r
+NEST-RL FER1_SPIOL -1 31 33 NEST-RL\r
+NEST-RL FER1_SPIOL -1 39 41 NEST-RL\r
+NEST-RL FER1_SPIOL -1 41 43 NEST-RL\r
+NEST-RL FER1_SPIOL -1 71 73 NEST-RL\r
+SCHELLMANN-LOOP-6 FER1_SPIOL -1 28 33 SCHELLMANN-LOOP-6\r
+SCHELLMANN-LOOP-6 FER1_SPIOL -1 68 73 SCHELLMANN-LOOP-6\r
+ST-MOTIF FER1_SPIOL -1 9 13 ST-MOTIF\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 76_8</a></html> FER1_MAIZE -1 76 80 ALPHA-BETA-MOTIF\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/alphabetamotif?gzip=false">ALPHA-BETA-MOTIF 77_8</a></html> FER1_MAIZE -1 77 81 ALPHA-BETA-MOTIF\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/betaturnir?gzip=false">BETA-TURN-IR 127_13</a></html> FER1_MAIZE -1 127 130 BETA-TURN-IR\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturnclassic?gzip=false">GAMMA-TURN-CLASSIC 113_11</a></html> FER1_MAIZE -1 113 115 GAMMA-TURN-CLASSIC\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturninverse?gzip=false">GAMMA-TURN-INVERSE 59_6</a></html> FER1_MAIZE -1 59 61 GAMMA-TURN-INVERSE\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/gammaturninverse?gzip=false">GAMMA-TURN-INVERSE 104_10</a></html> FER1_MAIZE -1 104 106 GAMMA-TURN-INVERSE\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 92_9</a></html> FER1_MAIZE -1 92 94 NEST-LR\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestlr?gzip=false">NEST-LR 94_9</a></html> FER1_MAIZE -1 94 96 NEST-LR\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 83_8</a></html> FER1_MAIZE -1 83 85 NEST-RL\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 91_9</a></html> FER1_MAIZE -1 91 93 NEST-RL\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 93_9</a></html> FER1_MAIZE -1 93 95 NEST-RL\r
+<html>Found in PDBs: 1gaq.B <a href="http://www.ebi.ac.uk/msd-srv/msdmotif/nestrl?gzip=false">NEST-RL 123_12</a></html> FER1_MAIZE -1 123 125 NEST-RL\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 132 136 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 174 178 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 175 179 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 180 184 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 181 185 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 214 218 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 215 219 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 218 222 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 223 227 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 246 250 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 251 255 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 254 258 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 258 262 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 279 283 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 280 284 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 289 293 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 296 300 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 299 303 ALPHA-BETA-MOTIF\r
+ASX-TURN-IIL FER1_MAIZE -1 160 162 ASX-TURN-IIL\r
+ASX-TURN-IIR FER1_MAIZE -1 107 109 ASX-TURN-IIR\r
+BETA-BULGE FER1_MAIZE -1 31 32 BETA-BULGE\r
+BETA-BULGE FER1_MAIZE -1 43 44 BETA-BULGE\r
+BETA-TURN-IIL FER1_MAIZE -1 170 173 BETA-TURN-IIL\r
+BETA-TURN-IIR FER1_MAIZE -1 71 74 BETA-TURN-IIR\r
+BETA-TURN-IIR FER1_MAIZE -1 140 143 BETA-TURN-IIR\r
+BETA-TURN-IIR FER1_MAIZE -1 274 277 BETA-TURN-IIR\r
+BETA-TURN-IL FER1_MAIZE -1 64 67 BETA-TURN-IL\r
+BETA-TURN-IR FER1_MAIZE -1 33 36 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 50 53 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 100 103 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 103 106 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 136 139 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 171 174 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 172 175 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 206 209 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 207 210 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 223 226 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 233 236 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 252 255 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 264 267 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 289 292 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 295 298 BETA-TURN-IR\r
+CATMAT-3 FER1_MAIZE -1 20 22 CATMAT-3\r
+CATMAT-3 FER1_MAIZE -1 47 49 CATMAT-3\r
+CATMAT-3 FER1_MAIZE -1 97 99 CATMAT-3\r
+CATMAT-4 FER1_MAIZE -1 189 192 CATMAT-4\r
+GAMMA-TURN-INVERSE FER1_MAIZE -1 68 70 GAMMA-TURN-INVERSE\r
+GAMMA-TURN-INVERSE FER1_MAIZE -1 84 86 GAMMA-TURN-INVERSE\r
+GAMMA-TURN-INVERSE FER1_MAIZE -1 232 234 GAMMA-TURN-INVERSE\r
+GAMMA-TURN-INVERSE FER1_MAIZE -1 240 242 GAMMA-TURN-INVERSE\r
+GAMMA-TURN-INVERSE FER1_MAIZE -1 244 246 GAMMA-TURN-INVERSE\r
+NEST-LR FER1_MAIZE -1 30 32 NEST-LR\r
+NEST-LR FER1_MAIZE -1 66 68 NEST-LR\r
+NEST-LR FER1_MAIZE -1 106 108 NEST-LR\r
+NEST-LR FER1_MAIZE -1 108 110 NEST-LR\r
+NEST-LR FER1_MAIZE -1 212 214 NEST-LR\r
+NEST-LR FER1_MAIZE -1 276 278 NEST-LR\r
+NEST-LR FER1_MAIZE -1 307 309 NEST-LR\r
+NEST-RL FER1_MAIZE -1 64 66 NEST-RL\r
+NEST-RL FER1_MAIZE -1 105 107 NEST-RL\r
+NEST-RL FER1_MAIZE -1 107 109 NEST-RL\r
+NEST-RL FER1_MAIZE -1 306 308 NEST-RL\r
+ST-TURN-IIL FER1_MAIZE -1 20 22 ST-TURN-IIL\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 24 28 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 25 29 ALPHA-BETA-MOTIF\r
+BETA-TURN-IR FER1_MAIZE -1 75 78 BETA-TURN-IR\r
+GAMMA-TURN-CLASSIC FER1_MAIZE -1 61 63 GAMMA-TURN-CLASSIC\r
+GAMMA-TURN-INVERSE FER1_MAIZE -1 7 9 GAMMA-TURN-INVERSE\r
+GAMMA-TURN-INVERSE FER1_MAIZE -1 52 54 GAMMA-TURN-INVERSE\r
+NEST-LR FER1_MAIZE -1 40 42 NEST-LR\r
+NEST-LR FER1_MAIZE -1 42 44 NEST-LR\r
+NEST-RL FER1_MAIZE -1 31 33 NEST-RL\r
+NEST-RL FER1_MAIZE -1 39 41 NEST-RL\r
+NEST-RL FER1_MAIZE -1 41 43 NEST-RL\r
+NEST-RL FER1_MAIZE -1 71 73 NEST-RL\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 176 180 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 233 237 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 247 251 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 278 282 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 286 290 ALPHA-BETA-MOTIF\r
+ALPHA-BETA-MOTIF FER1_MAIZE -1 295 299 ALPHA-BETA-MOTIF\r
+ASX-MOTIF FER1_MAIZE -1 122 126 ASX-MOTIF\r
+ASX-MOTIF FER1_MAIZE -1 160 164 ASX-MOTIF\r
+ASX-TURN-IR FER1_MAIZE -1 122 124 ASX-TURN-IR\r
+BETA-BULGE-LOOP-5 FER1_MAIZE -1 122 126 BETA-BULGE-LOOP-5\r
+BETA-BULGE-LOOP-5 FER1_MAIZE -1 239 243 BETA-BULGE-LOOP-5\r
+BETA-TURN-IR FER1_MAIZE -1 122 125 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 160 163 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 239 242 BETA-TURN-IR\r
+BETA-TURN-IR FER1_MAIZE -1 261 264 BETA-TURN-IR\r
+CATMAT-3 FER1_MAIZE -1 80 82 CATMAT-3\r
+CATMAT-3 FER1_MAIZE -1 87 89 CATMAT-3\r
+CATMAT-3 FER1_MAIZE -1 262 264 CATMAT-3\r
+NEST-RL FER1_MAIZE -1 124 126 NEST-RL\r
+NEST-RL FER1_MAIZE -1 241 243 NEST-RL\r
+NEST-RL FER1_MAIZE -1 292 294 NEST-RL\r
+ENDGROUP s3dm\r
--- /dev/null
+(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+ </tr>
+ <tr>
+ <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
+ history</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
+ Code</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
+ Mailing List</a></td>
+ </tr>
+ <tr>
+ <td align="left" valign="middle"><a
+ href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
+ class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
+ bug reports to the discussion list.</em></td>
+ </tr>
+ <tr></tr>
+ <tr>
+ <!--<td align="left" valign="middle"><br>
+ Please send problems<br>and
+ bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
+ </tr>
+ </table>
+ </div>
+ <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
+ <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
+ </div>
+ </td>
+ <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
+ <p> </p>
+ Click the Javascript buttons below to interact with the Applet
+ instance on the page.<br>
+ View the source in your browser to see how it has been done.<br>
+ The applet's public API methods are <a href="#api">listed below</a>
+ the following example.<br>
+ <applet code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar" name="Jalview">
+ <param name="file" value="plantfdx.fa">
+ <param name="features" value="plantfdx.features">
+ <param name="wrap" value="true">
+ <param name="showAnnotation" value="false">
+ <param name="windowHeight" value="500">
+ <param name="windowWidth" value="650">
+ <param name="showFullId" value="false">
+ <param name="RGB" value="F2F2FF">
+ <param name="linkLabel_1" value="SRS">
+ <param name="linkUrl_1"
+ value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
+ <param name="linkLabel_2" value="Uniprot">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="hidefeaturegroups" value="uniprot" />
+ <param name="showbutton" value="false" />
+ </applet>
+ <form name="exampleForm"><br>
+ <br>
+ <center><strong>Using the Jalview Applet for Input
+ to an HTML Form</strong></center>
+ <div align="center"><input type="button"
+ onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
+ value="Fill Form from Jalview" /> <br>
+ <br>
+ <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
+ </form>
+ <center><strong>Make a new View and Get and Set
+ Group Display List</strong></center>
+ <form name="groupForm">
+ <div align="center"><input type="button"
+ onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
+ value="Get groups" /> <input type="button"
+ onClick="document.applets.Jalview.newView()" value="new View" /> <br>
+ <textarea name="groups" cols="55" rows="9"></textarea> <br>
+ <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
+ value="Display groups" /> <input type="button"
+ onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
+ value="Hide groups" /></div>
+ </form>
+ <p><a name="api" /> Since Jalview 2.5, the public methods listed
+ below are available to be called via Javascript.</p>
+ <p>Unfortunately Javascript - Java communication is not possible
+ using Internet Explorer or Opera on Macs. Please use Safari or
+ Firefox.</p>
+ <p>If more than one Jalview window is open, Jalview returns the
+ alignment in the active window, unless you provide an AlignFrame
+ object reference.</p>
+ <p>The alignment output format can be either Fasta, PFAM, Clustal,
+ MSF, PIR, or BLC.</p>
+ <p>When referring to the Jalview applet in javascript, you must
+ either give Jalview a name in the applet tag or use the applets index.</p>
+
+ <pre>//get list of IDs of selected sequences
+public String getSelectedSequences()
+
+// list of IDs of selected sequences terminated by sep or, if sep is null, '¬' (&#172;)
+public String getSelectedSequences(sep)
+
+// get selected sequences as alignment as format with or without start-end suffix
+public String getSelectedSequencesAsAlignment(String format, boolean suffix)
+
+// get selected sequences as alignment from given view as format with or without start-end suffix
+public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, boolean suffix)
+
+// get alignment as format
+public String getAlignment(String format)
+
+// get alignment as format with jalview
+// start-end sequence suffix appended
+public String getAlignment(String format, String suffix)
+
+// get alignment displayed in alf as format
+public String getAlignmentFrom(AlignFrame alf, String format)
+
+// get alignment displayed in alf as format
+// with jalview start-end sequence suffix appended
+public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
+
+// add the given features or annotation to the current alignment
+public void loadAnnotation(String annotation)
+
+// add the given features or annotation to the given alignment view
+public void loadAnnotationFrom(AlignFrame alf, String annotation)
+
+// get the sequence features in the given format (Jalview or GFF)
+public String getFeatures(String format)
+
+// get the sequence features in alf in the given format (Jalview or GFF)
+public String getFeaturesFrom(AlignFrame alf, String format)
+
+// get current alignment's annotation as an annotation file
+public String getAnnotation()
+
+// get alignment view alf's annotation as an annotation file
+public String getAnnotationFrom(AlignFrame alf)
+
+// create a new view and return the alignFrame instance
+public AlignFrame newView()
+
+// create a new view named name and return the alignFrame instance
+public AlignFrame newView(String name)
+
+// create a new view on alf and return the alignFrame instance
+public AlignFrame newViewFrom(AlignFrame alf)
+
+// create a new view named name on alf
+// and return the alignFrame instance
+public AlignFrame newViewFrom(AlignFrame alf, String name)
+
+// load a new alignment
+public AlignFrame loadAlignment(String text, String title)
+
+// return separator separated list of feature groups
+// on the current alignment
+public String getFeatureGroups()
+
+// return separator separated list of feature groups on alf
+public String getFeatureGroupsOn(AlignFrame alf)
+
+// return separator separated list of feature groups
+// either visible or hidden
+public String getFeatureGroupsOfState(boolean state)
+
+// return separator separated list of feature groups
+// either visible or hidden on alf
+public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean state)
+
+// set the separator separated list of feature groups as
+// visible or hidden on the current alignment
+public void setFeatureGroupState(String groupList, boolean state)
+
+// set the separator separated list of feature groups
+// as visible or hidden on alf
+public void setFeatureGroupStateOn(AlignFrame alf, String groupList, boolean state)
+
+// helper functions
+
+// convert list to a separator separated array
+public String arrayToSeparatorList(String[] list)
+
+// get a string array from a list
+public String[] separatorListToArray(String list)
+
+// get the current separator
+public String getSeparator()
+
+// set the current separator
+public void setSeparator(String)
+
+//// JalviewLite global state methods and fields
+
+// return the build date as a string
+public static String getBuildDate()
+
+// return the JalviewLite version as a string
+public static String getVersion()
+
+// debug flag - controls output to standard out
+public static boolean debug
+
+</pre> <!-- InstanceEndEditable --></td>
+ </tr>
+ </table>
+</div>
+</body>
+<!-- InstanceEnd --></html>
--- /dev/null
+>FER_CAPAA Ferredoxin
+ASYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEG
+WVLTCVAYPQSDVTIETHKEAELVG-
+>FER_CAPAN Ferredoxin, chloroplast precursor
+ASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEG
+WVLTCVAYPQSDVTIETHKEAELVG-
+>FER1_SOLLC Ferredoxin-1, chloroplast precursor
+ASYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAG
+FVLTCVAYPKGDVTIETHKEEELTA-
+>Q93XJ9_SOLTU Ferredoxin I precursor
+ASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAG
+FVLTCVAYPKCDVTIETHKEEELTA-
+>FER1_MESCR Ferredoxin-1, chloroplast precursor
+AAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEG
+WVLTCVAYPTGDVTIETHKEEELTA-
+>FER1_SPIOL Ferredoxin-1, chloroplast precursor
+AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEG
+WVLTCAAYPVSDVTIETHKEEELTA-
+>FER1_ARATH Ferredoxin-1, chloroplast precursor
+ATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEG
+FVLTCAAYPTSDVTIETHKEEDIV--
+>FER2_ARATH Ferredoxin-2, chloroplast precursor
+ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEG
+YVLTCVAYPTSDVVIETHKEEAIM--
+>FER1_PEA Ferredoxin-1, chloroplast precursor
+ASYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAG
+FVLTCVAYPTSDVVIETHKEEDLTA-
+>Q7XA98_TRIPR Ferredoxin I
+ATYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGG
+WVLTCVAFPTSDVTIETHKEEELTA-
+>FER1_MAIZE Ferredoxin-1, chloroplast precursor
+ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADG
+WVLTCHAYPTSDVVIETHKEEELTGA
+>O80429_MAIZE Ferredoxin
+ATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADG
+WVLTCAAYPTSDVVIETHKEDDLL--
+>Q93Z60_ARATH At1g10960/T19D16_12
+ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------
+--------------------------
+>FER3_RAPSA Ferredoxin, leaf L-A
+ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEG
+FVLTCAAYPTSDVTIETHREEDMV--
+>FER_BRANA Ferredoxin
+ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEG
+FVLTCAAYPTSDVTIETHKEEELV--
--- /dev/null
+Lupas_21:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+Lupas_14:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+Lupas_28:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
+
+jnetpred:-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,-,-,-,-,E,E,E,E,E,-,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,-,-,E,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,E,E,E,E,-,-,-,-,E,E,E,E,-,
+JNETCONF:1,3,1,2,7,7,9,9,7,1,6,8,9,8,1,3,5,5,1,6,8,9,7,4,8,8,7,2,3,2,0,2,1,2,5,7,8,8,7,6,4,2,1,3,5,7,8,7,5,4,4,5,7,5,2,5,5,1,4,2,0,1,5,6,7,7,5,4,5,4,5,6,6,3,1,1,1,4,6,1,6,9,9,9,8,8,7,0,8,9,9,7,2,8,9,9,8,
+JNETSOL25:B,-,B,-,-,B,B,B,B,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,B,B,B,-,B,-,B,-,-,-,-,-,-,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,B,B,-,-,-,-,-,-,B,-,-,B,B,B,B,B,B,B,B,B,B,-,-,-,-,B,B,-,-,
+JNETSOL5:-,-,-,-,-,-,-,B,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,B,B,B,B,B,-,-,-,-,-,-,-,B,-,-,
+JNETSOL0:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,
+JNETPROPH:0.44514,0.02676,0.50891,0.59931,0.03767,0.31300,0.54697,0.01490,0.41391,0.55820,0.01816,0.38620,0.82780,0.00804,0.16764,0.86436,0.00416,0.14111,0.96423,0.00391,0.03569,0.94587,0.00483,0.05758,0.88110,0.01273,0.13718,0.57335,0.02654,0.44509,0.17935,0.02373,0.80108,0.08085,0.00825,0.91351,0.06739,0.00450,0.93803,0.11202,0.00730,0.88142,0.41953,0.00953,0.55868,0.64171,0.00894,0.34807,0.74660,0.00831,0.27522,0.78367,0.00952,0.27786,0.54376,0.01578,0.49285,0.18080,0.01695,0.78463,0.05922,0.01157,0.90794,0.03565,0.02045,0.91548,0.12377,0.02896,0.77671,0.58102,0.05600,0.22143,0.82750,0.03376,0.07013,0.86371,0.02169,0.08984,0.81881,0.04410,0.14200,0.60784,0.05837,0.36725,0.27275,0.10034,0.53452,0.12405,0.28672,0.44961,0.07683,0.43094,0.40783,0.05134,0.55252,0.37353,0.03890,
+JNETPROPB:0.59931,0.03767,0.31300,0.54697,0.01490,0.41391,0.55820,0.01816,0.38620,0.82780,0.00804,0.16764,0.86436,0.00416,0.14111,0.96423,0.00391,0.03569,0.94587,0.00483,0.05758,0.88110,0.01273,0.13718,0.57335,0.02654,0.44509,0.17935,0.02373,0.80108,0.08085,0.00825,0.91351,0.06739,0.00450,0.93803,0.11202,0.00730,0.88142,0.41953,0.00953,0.55868,0.64171,0.00894,0.34807,0.74660,0.00831,0.27522,0.78367,0.00952,0.27786,0.54376,0.01578,0.49285,0.18080,0.01695,0.78463,0.05922,0.01157,0.90794,0.03565,0.02045,0.91548,0.12377,0.02896,0.77671,0.58102,0.05600,0.22143,0.82750,0.03376,0.07013,0.86371,0.02169,0.08984,0.81881,0.04410,0.14200,0.60784,0.05837,0.36725,0.27275,0.10034,0.53452,0.12405,0.28672,0.44961,0.07683,0.43094,0.40783,0.05134,0.55252,0.37353,0.03890,0.52815,0.46401,0.03979,
+JNETPROPC:0.54697,0.01490,0.41391,0.55820,0.01816,0.38620,0.82780,0.00804,0.16764,0.86436,0.00416,0.14111,0.96423,0.00391,0.03569,0.94587,0.00483,0.05758,0.88110,0.01273,0.13718,0.57335,0.02654,0.44509,0.17935,0.02373,0.80108,0.08085,0.00825,0.91351,0.06739,0.00450,0.93803,0.11202,0.00730,0.88142,0.41953,0.00953,0.55868,0.64171,0.00894,0.34807,0.74660,0.00831,0.27522,0.78367,0.00952,0.27786,0.54376,0.01578,0.49285,0.18080,0.01695,0.78463,0.05922,0.01157,0.90794,0.03565,0.02045,0.91548,0.12377,0.02896,0.77671,0.58102,0.05600,0.22143,0.82750,0.03376,0.07013,0.86371,0.02169,0.08984,0.81881,0.04410,0.14200,0.60784,0.05837,0.36725,0.27275,0.10034,0.53452,0.12405,0.28672,0.44961,0.07683,0.43094,0.40783,0.05134,0.55252,0.37353,0.03890,0.52815,0.46401,0.03979,0.40515,0.56556,0.03815,
+JNETHMM:-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,-,-,-,-,E,E,E,E,E,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,-,-,E,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,E,E,E,E,-,-,-,-,E,E,E,E,-,
+JNETALIGN:-,-,-,E,E,E,E,E,-,-,-,-,-,-,E,-,-,-,-,-,-,E,E,E,E,H,H,H,H,H,-,-,-,-,-,-,-,E,-,-,-,-,-,-,-,-,-,-,-,-,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,-,-,-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,E,E,H,H,H,-,-,-,-,
+align1;Sequence0/1.97:A,S,Y,K,V,K,L,I,T,P,D,G,P,I,E,F,D,C,P,D,D,V,Y,I,L,D,Q,A,E,E,A,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,I,A,G,G,A,V,D,Q,T,D,G,N,F,L,D,D,D,Q,L,E,E,G,W,V,L,T,C,V,A,Y,P,Q,S,D,V,T,I,E,T,H,K,E,A,E,L,V,G,
+align2;Sequence1/1.144:A,S,Y,K,V,K,L,I,T,P,D,G,P,I,E,F,D,C,P,D,N,V,Y,I,L,D,Q,A,E,E,A,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,I,A,G,G,A,V,D,Q,T,D,G,N,F,L,D,D,D,Q,L,E,E,G,W,V,L,T,C,V,A,Y,P,Q,S,D,V,T,I,E,T,H,K,E,A,E,L,V,G,
+align3;Sequence2/1.144:A,S,Y,K,V,K,L,I,T,P,E,G,P,I,E,F,E,C,P,D,D,V,Y,I,L,D,Q,A,E,E,E,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,T,A,G,S,V,D,Q,S,D,G,N,F,L,D,E,D,Q,E,A,A,G,F,V,L,T,C,V,A,Y,P,K,G,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align4;Sequence3/1.144:A,S,Y,K,V,K,L,I,T,P,D,G,P,I,E,F,E,C,P,D,D,V,Y,I,L,D,Q,A,E,E,E,G,H,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,T,A,G,T,V,D,Q,S,D,G,K,F,L,D,D,D,Q,E,A,A,G,F,V,L,T,C,V,A,Y,P,K,C,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align5;Sequence4/1.149:A,S,Y,K,V,K,L,V,T,P,D,G,T,Q,E,F,E,C,P,S,D,V,Y,I,L,D,H,A,E,E,V,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,G,G,E,V,D,Q,S,D,G,S,F,L,D,D,E,Q,I,E,A,G,F,V,L,T,C,V,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,E,D,L,T,A,
+align6;Sequence5/1.152:A,T,Y,K,V,K,L,I,T,P,E,G,P,Q,E,F,D,C,P,D,D,V,Y,I,L,D,H,A,E,E,V,G,I,E,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,N,G,N,V,N,Q,E,D,G,S,F,L,D,D,E,Q,I,E,G,G,W,V,L,T,C,V,A,F,P,T,S,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align7;Sequence6/1.148:A,A,Y,K,V,T,L,V,T,P,E,G,K,Q,E,L,E,C,P,D,D,V,Y,I,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,T,S,G,S,V,N,Q,D,D,G,S,F,L,D,D,D,Q,I,K,E,G,W,V,L,T,C,V,A,Y,P,T,G,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align8;Sequence7/1.147:A,A,Y,K,V,T,L,V,T,P,T,G,N,V,E,F,Q,C,P,D,D,V,Y,I,L,D,A,A,E,E,E,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,L,K,T,G,S,L,N,Q,D,D,Q,S,F,L,D,D,D,Q,I,D,E,G,W,V,L,T,C,A,A,Y,P,V,S,D,V,T,I,E,T,H,K,E,E,E,L,T,A,
+align9;Sequence8/1.96:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,D,D,D,V,Y,V,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,F,L,D,D,D,Q,I,A,E,G,F,V,L,T,C,A,A,Y,P,T,S,D,V,T,I,E,T,H,R,E,E,D,M,V,.,
+align10;Sequence9/1.148:A,T,Y,K,V,K,F,I,T,P,E,G,E,L,E,V,E,C,D,D,D,V,Y,V,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,F,L,D,D,E,Q,I,G,E,G,F,V,L,T,C,A,A,Y,P,T,S,D,V,T,I,E,T,H,K,E,E,D,I,V,.,
+align11;Sequence10/1.96:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,D,D,D,V,Y,V,L,D,A,A,E,E,A,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,F,V,D,Q,S,D,E,S,F,L,D,D,D,Q,I,A,E,G,F,V,L,T,C,A,A,Y,P,T,S,D,V,T,I,E,T,H,K,E,E,E,L,V,.,
+align12;Sequence11/1.148:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,E,E,D,V,Y,V,L,D,A,A,E,E,A,G,L,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,I,D,Q,S,D,Q,S,F,L,D,D,E,Q,M,S,E,G,Y,V,L,T,C,V,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,E,A,I,M,.,
+align13;Sequence12/1.118:A,T,Y,K,V,K,F,I,T,P,E,G,E,Q,E,V,E,C,E,E,D,V,Y,V,L,D,A,A,E,E,A,G,L,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,I,D,Q,S,D,Q,S,F,L,D,D,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,.,
+align14;Sequence13/1.150:A,T,Y,N,V,K,L,I,T,P,E,G,E,V,E,L,Q,V,P,D,D,V,Y,I,L,D,Q,A,E,E,D,G,I,D,L,P,Y,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,Y,L,D,D,G,Q,I,A,D,G,W,V,L,T,C,H,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,E,E,L,T,G,
+align15;Sequence14/1.140:A,T,Y,N,V,K,L,I,T,P,E,G,E,V,E,L,Q,V,P,D,D,V,Y,I,L,D,F,A,E,E,E,G,I,D,L,P,F,S,C,R,A,G,S,C,S,S,C,A,G,K,V,V,S,G,S,V,D,Q,S,D,Q,S,F,L,N,D,N,Q,V,A,D,G,W,V,L,T,C,A,A,Y,P,T,S,D,V,V,I,E,T,H,K,E,D,D,L,L,.,
+jpred:-,-,-,-,E,E,E,E,E,E,-,-,-,-,-,E,E,E,E,-,-,-,-,E,E,E,E,E,-,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,-,-,E,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,E,E,E,E,E,E,-,-,-,-,E,E,E,E,-,
--- /dev/null
+>FER_CAPAA/1-97
+----------------------------------------------------------ASYKVKLITPDGPI
+EFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVT
+IETHKEAELVG-
+>FER_CAPAN/1-144
+------MASVSATMISTSFMPRKPAVTSLKPIP-NVG-EALFGLKS---ANGGKVTCMASYKVKLITPDGPI
+EFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDVT
+IETHKEAELVG-
+>FER1_SOLLC/1-144
+------MASISGTMISTSFLPRKPAVTSLKAIS-NVG-EALFGLKS---GRNGRITCMASYKVKLITPEGPI
+EFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDVT
+IETHKEEELTA-
+>Q93XJ9_SOLTU/1-144
+------MASISGTMISTSFLPRKPVVTSLKAIS-NVG-EALFGLKS---GRNGRITCMASYKVKLITPDGPI
+EFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVT
+IETHKEEELTA-
+>FER1_PEA/1-149
+---MATTPALYGTAVSTSFLRTQPMPMSVTTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGTQ
+EFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDVV
+IETHKEEDLTA-
+>Q7XA98_TRIPR/1-152
+---MATTPALYGTAVSTSFMRRQPVPMSVATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGPQ
+EFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDVT
+IETHKEEELTA-
+>FER1_MESCR/1-148
+--MAATTAALSGATMSTAFAPKT--PPMTAALPTNVG-RALFGLKS--SASRGRVTAMAAYKVTLVTPEGKQ
+ELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDVT
+IETHKEEELTA-
+>FER1_SPIOL/1-147
+----MAATTTTMMGMATTFVPKPQAPPMMAALPSNTG-RSLFGLKT--GSRGGRMT-MAAYKVTLVTPTGNV
+EFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVT
+IETHKEEELTA-
+>FER3_RAPSA/1-96
+----------------------------------------------------------ATYKVKFITPEGEQ
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVT
+IETHREEDMV--
+>FER1_ARATH/1-148
+----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
+IETHKEEDIV--
+>FER_BRANA/1-96
+----------------------------------------------------------ATYKVKFITPEGEQ
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT
+IETHKEEELV--
+>FER2_ARATH/1-148
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
+IETHKEEAIM--
+>Q93Z60_ARATH/1-118
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD--------------------
+------------
+>FER1_MAIZE/1-150
+MATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVG---IMGRSA---SSRRRLRAQATYNVKLITPEGEV
+ELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVV
+IETHKEEELTGA
+>O80429_MAIZE/1-140
+---------MAATALSMSILRAPP-PCFSSPLRLRVAVAKPLAAPM----RRQLLRAQATYNVKLITPEGEV
+ELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVV
+IETHKEDDLL--
--- /dev/null
+HELIX d4d189
+MOD_RES 47e459
+TRANSIT 6f949b
+TURN 1d1e2d
+METAL 70686e
+SIGNAL 92c7dd
+VARIANT 60beac
+Pfam dc206a
+CONFLICT c46c6e
+STRAND 25c54c
+
+STARTGROUP uniprot
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 8_83</a></html> FER_CAPAA -1 8 83 Pfam
+Chloroplast FER_CAPAN -1 1 47 TRANSIT
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL
+Phosphothreonine FER_CAPAN -1 136 136 MOD_RES
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 55_130</a></html> FER_CAPAN -1 55 130 Pfam
+Chloroplast FER1_SOLLC -1 1 47 TRANSIT
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL
+Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 55_130</a></html> FER1_SOLLC -1 55 130 Pfam
+Evidence: EI4 Q93XJ9_SOLTU -1 1 48 SIGNAL
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 55_130</a></html> Q93XJ9_SOLTU -1 55 130 Pfam
+Chloroplast FER1_PEA -1 1 52 TRANSIT
+L -> I (in strain: cv. Onward) FER1_PEA -1 59 59 VARIANT
+I -> L (in strain: cv. Onward) FER1_PEA -1 85 85 VARIANT
+Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL
+YPTS -> PPPA (in Ref. 2) FER1_PEA -1 132 135 CONFLICT
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 60_135</a></html> FER1_PEA -1 60 135 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 63_138</a></html> Q7XA98_TRIPR -1 63 138 Pfam
+Chloroplast FER1_MESCR -1 1 51 TRANSIT
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL
+Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 59_134</a></html> FER1_MESCR -1 59 134 Pfam
+Chloroplast FER1_SPIOL -1 1 50 TRANSIT
+STRAND FER1_SPIOL -1 52 59 STRAND
+TURN FER1_SPIOL -1 60 61 TURN
+STRAND FER1_SPIOL -1 62 69 STRAND
+TURN FER1_SPIOL -1 70 71 TURN
+HELIX FER1_SPIOL -1 74 80 HELIX
+TURN FER1_SPIOL -1 81 82 TURN
+STRAND FER1_SPIOL -1 88 92 STRAND
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL
+TURN FER1_SPIOL -1 96 97 TURN
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL
+STRAND FER1_SPIOL -1 98 104 STRAND
+TURN FER1_SPIOL -1 109 110 TURN
+HELIX FER1_SPIOL -1 116 121 HELIX
+TURN FER1_SPIOL -1 122 122 TURN
+STRAND FER1_SPIOL -1 123 125 STRAND
+HELIX FER1_SPIOL -1 126 128 HELIX
+Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL
+STRAND FER1_SPIOL -1 130 133 STRAND
+STRAND FER1_SPIOL -1 135 138 STRAND
+HELIX FER1_SPIOL -1 142 144 HELIX
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 58_133</a></html> FER1_SPIOL -1 58 133 Pfam
+I -> V FER3_RAPSA -1 8 8 VARIANT
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL
+S -> T FER3_RAPSA -1 55 55 VARIANT
+Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL
+R -> K FER3_RAPSA -1 91 91 VARIANT
+M -> V FER3_RAPSA -1 95 95 VARIANT
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 8_83</a></html> FER3_RAPSA -1 8 83 Pfam
+Chloroplast FER1_ARATH -1 1 52 TRANSIT
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 60_135</a></html> FER1_ARATH -1 60 135 Pfam
+Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL
+Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 8_83</a></html> FER_BRANA -1 8 83 Pfam
+Chloroplast FER2_ARATH -1 1 52 TRANSIT
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL
+Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 60_135</a></html> FER2_ARATH -1 60 135 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 60_118</a></html> Q93Z60_ARATH -1 60 118 Pfam
+Chloroplast FER1_MAIZE -1 1 52 TRANSIT
+STRAND FER1_MAIZE -1 57 59 STRAND
+STRAND FER1_MAIZE -1 72 74 STRAND
+HELIX FER1_MAIZE -1 76 80 HELIX
+TURN FER1_MAIZE -1 81 84 TURN
+STRAND FER1_MAIZE -1 90 97 STRAND
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL
+TURN FER1_MAIZE -1 98 99 TURN
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL
+TURN FER1_MAIZE -1 118 119 TURN
+HELIX FER1_MAIZE -1 120 123 HELIX
+TURN FER1_MAIZE -1 128 129 TURN
+Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL
+STRAND FER1_MAIZE -1 132 135 STRAND
+STRAND FER1_MAIZE -1 137 141 STRAND
+TURN FER1_MAIZE -1 142 142 TURN
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 60_135</a></html> FER1_MAIZE -1 60 135 Pfam
+<html>Description: Fer2 Status: True Positive <a href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam 52_127</a></html> O80429_MAIZE -1 52 127 Pfam
+ENDGROUP uniprot
--- /dev/null
+>FER_CAPAA Ferredoxin\r
+-----------------------------------------------------------ASYKVKLITPDGP\r
+IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV\r
+TIETHKEAELVG-\r
+>FER_CAPAN Ferredoxin, chloroplast precursor\r
+MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP\r
+IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV\r
+TIETHKEAELVG-\r
+>FER1_SOLLC Ferredoxin-1, chloroplast precursor\r
+MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP\r
+IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV\r
+TIETHKEEELTA-\r
+>Q93XJ9_SOLTU Ferredoxin I precursor\r
+MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP\r
+IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV\r
+TIETHKEEELTA-\r
+>FER1_PEA Ferredoxin-1, chloroplast precursor\r
+MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT\r
+QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV\r
+VIETHKEEDLTA-\r
+>Q7XA98_TRIPR Ferredoxin I\r
+MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP\r
+QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV\r
+TIETHKEEELTA-\r
+>FER1_MESCR Ferredoxin-1, chloroplast precursor\r
+MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK\r
+QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV\r
+TIETHKEEELTA-\r
+>FER1_SPIOL Ferredoxin-1, chloroplast precursor\r
+MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN\r
+VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV\r
+TIETHKEEELTA-\r
+>FER3_RAPSA Ferredoxin, leaf L-A\r
+-----------------------------------------------------------ATYKVKFITPEGE\r
+QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV\r
+TIETHREEDMV--\r
+>FER1_ARATH Ferredoxin-1, chloroplast precursor\r
+MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE\r
+LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV\r
+TIETHKEEDIV--\r
+>FER_BRANA Ferredoxin\r
+-----------------------------------------------------------ATYKVKFITPEGE\r
+QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV\r
+TIETHKEEELV--\r
+>FER2_ARATH Ferredoxin-2, chloroplast precursor\r
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE\r
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV\r
+VIETHKEEAIM--\r
+>Q93Z60_ARATH At1g10960/T19D16_12\r
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE\r
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------\r
+-------------\r
+>FER1_MAIZE Ferredoxin-1, chloroplast precursor\r
+MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE\r
+VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV\r
+VIETHKEEELTGA\r
+>O80429_MAIZE Ferredoxin\r
+MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE\r
+VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV\r
+VIETHKEDDLL--\r
git://source.jalview.org / jalview.git / commitdiff