| Chromista |
| ID: | 1463626961 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 800 (796) | ||
| Sequences: | 6671 (3181) | ||
| Seq/Len: | 8.381 | ||
| Nf(neff/√len): | 112.7 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 8.381).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 137_D | 202_R | 5.905 | 1.00 |
| 729_K | 752_L | 5.538 | 1.00 |
| 309_T | 337_A | 4.897 | 1.00 |
| 135_G | 204_I | 4.739 | 1.00 |
| 725_K | 753_E | 4.462 | 1.00 |
| 721_Y | 757_K | 3.968 | 1.00 |
| 784_R | 789_T | 3.941 | 1.00 |
| 650_R | 658_T | 3.896 | 1.00 |
| 306_V | 337_A | 3.602 | 1.00 |
| 517_R | 520_E | 3.398 | 1.00 |
| 519_S | 526_S | 3.280 | 1.00 |
| 233_K | 270_E | 3.259 | 1.00 |
| 513_Q | 516_Q | 3.183 | 1.00 |
| 668_M | 710_L | 3.159 | 1.00 |
| 552_C | 646_F | 3.134 | 1.00 |
| 209_G | 261_L | 2.946 | 1.00 |
| 305_S | 308_D | 2.875 | 1.00 |
| 310_V | 333_L | 2.856 | 1.00 |
| 514_L | 573_E | 2.854 | 1.00 |
| 136_V | 141_Q | 2.766 | 1.00 |
| 484_T | 487_D | 2.759 | 1.00 |
| 467_D | 471_A | 2.730 | 1.00 |
| 732_I | 747_A | 2.715 | 1.00 |
| 382_Q | 407_L | 2.677 | 1.00 |
| 515_P | 530_E | 2.660 | 1.00 |
| 534_N | 779_T | 2.652 | 1.00 |
| 129_D | 132_N | 2.616 | 1.00 |
| 328_I | 361_C | 2.550 | 1.00 |
| 534_N | 783_K | 2.487 | 1.00 |
| 733_D | 736_N | 2.439 | 1.00 |
| 720_G | 723_Q | 2.409 | 1.00 |
| 128_Y | 132_N | 2.349 | 1.00 |
| 137_D | 140_K | 2.346 | 1.00 |
| 755_I | 772_Y | 2.334 | 1.00 |
| 521_K | 572_L | 2.329 | 1.00 |
| 158_V | 299_V | 2.309 | 1.00 |
| 216_K | 220_E | 2.299 | 1.00 |
| 515_P | 537_L | 2.296 | 1.00 |
| 721_Y | 753_E | 2.295 | 1.00 |
| 441_T | 460_L | 2.289 | 1.00 |
| 567_A | 667_I | 2.250 | 1.00 |
| 672_L | 701_H | 2.247 | 1.00 |
| 449_K | 461_Q | 2.212 | 1.00 |
| 230_N | 234_Q | 2.206 | 1.00 |
| 456_R | 459_D | 2.205 | 1.00 |
| 375_I | 414_L | 2.192 | 1.00 |
| 161_I | 299_V | 2.186 | 1.00 |
| 306_V | 341_H | 2.183 | 1.00 |
| 438_V | 465_L | 2.177 | 1.00 |
| 758_D | 776_A | 2.174 | 1.00 |
| 735_L | 773_I | 2.167 | 1.00 |
| 582_V | 624_N | 2.152 | 1.00 |
| 592_K | 637_D | 2.146 | 1.00 |
| 356_L | 492_V | 2.145 | 1.00 |
| 211_L | 228_V | 2.142 | 1.00 |
| 556_L | 670_S | 2.110 | 1.00 |
| 455_A | 459_D | 2.105 | 1.00 |
| 554_L | 710_L | 2.095 | 1.00 |
| 523_V | 730_L | 2.093 | 1.00 |
| 83_I | 106_A | 2.070 | 1.00 |
| 284_K | 610_E | 2.034 | 1.00 |
| 672_L | 698_I | 2.011 | 1.00 |
| 171_V | 246_M | 2.009 | 1.00 |
| 521_K | 569_K | 1.998 | 1.00 |
| 529_I | 566_L | 1.996 | 1.00 |
| 593_H | 602_P | 1.982 | 1.00 |
| 517_R | 573_E | 1.970 | 1.00 |
| 698_I | 707_L | 1.970 | 1.00 |
| 246_M | 286_V | 1.969 | 1.00 |
| 505_T | 513_Q | 1.945 | 1.00 |
| 390_T | 393_E | 1.940 | 1.00 |
| 130_A | 227_A | 1.934 | 1.00 |
| 334_V | 338_K | 1.919 | 1.00 |
| 389_Q | 404_K | 1.917 | 1.00 |
| 386_E | 411_R | 1.914 | 1.00 |
| 512_I | 786_I | 1.906 | 1.00 |
| 645_V | 666_I | 1.899 | 1.00 |
| 521_K | 565_E | 1.894 | 1.00 |
| 145_I | 189_N | 1.894 | 1.00 |
| 447_A | 451_V | 1.894 | 1.00 |
| 555_F | 667_I | 1.884 | 1.00 |
| 230_N | 233_K | 1.882 | 1.00 |
| 724_M | 756_M | 1.861 | 1.00 |
| 754_K | 758_D | 1.847 | 1.00 |
| 772_Y | 776_A | 1.831 | 1.00 |
| 311_S | 314_R | 1.820 | 1.00 |
| 336_A | 357_V | 1.815 | 1.00 |
| 335_L | 485_A | 1.812 | 1.00 |
| 197_E | 200_R | 1.808 | 1.00 |
| 590_M | 594_S | 1.786 | 1.00 |
| 580_H | 621_R | 1.784 | 1.00 |
| 434_L | 468_L | 1.776 | 1.00 |
| 364_I | 483_V | 1.760 | 1.00 |
| 593_H | 596_S | 1.749 | 1.00 |
| 618_V | 664_T | 1.749 | 1.00 |
| 731_Q | 734_E | 1.747 | 1.00 |
| 527_A | 717_N | 1.743 | 1.00 |
| 645_V | 651_L | 1.734 | 1.00 |
| 546_E | 738_R | 1.731 | 1.00 |
| 441_T | 465_L | 1.731 | 1.00 |
| 405_E | 409_E | 1.722 | 1.00 |
| 48_C | 53_V | 1.721 | 1.00 |
| 747_A | 751_A | 1.718 | 1.00 |
| 302_G | 621_R | 1.718 | 1.00 |
| 314_R | 330_D | 1.716 | 1.00 |
| 527_A | 691_K | 1.714 | 1.00 |
| 306_V | 338_K | 1.710 | 1.00 |
| 146_D | 165_R | 1.702 | 1.00 |
| 340_S | 349_L | 1.697 | 1.00 |
| 430_E | 471_A | 1.695 | 1.00 |
| 433_R | 437_K | 1.687 | 1.00 |
| 521_K | 578_E | 1.687 | 1.00 |
| 725_K | 749_D | 1.679 | 1.00 |
| 618_V | 661_F | 1.674 | 1.00 |
| 732_I | 773_I | 1.673 | 1.00 |
| 731_Q | 770_K | 1.667 | 1.00 |
| 728_M | 752_L | 1.667 | 1.00 |
| 306_V | 310_V | 1.666 | 1.00 |
| 717_N | 723_Q | 1.644 | 1.00 |
| 444_K | 456_R | 1.629 | 1.00 |
| 513_Q | 517_R | 1.618 | 1.00 |
| 243_I | 273_V | 1.605 | 1.00 |
| 250_L | 292_F | 1.605 | 1.00 |
| 130_A | 231_E | 1.604 | 1.00 |
| 695_M | 698_I | 1.590 | 1.00 |
| 310_V | 334_V | 1.588 | 1.00 |
| 507_D | 540_R | 1.577 | 1.00 |
| 360_A | 491_V | 1.573 | 1.00 |
| 725_K | 752_L | 1.571 | 1.00 |
| 728_M | 756_M | 1.571 | 1.00 |
| 747_A | 752_L | 1.569 | 1.00 |
| 208_L | 211_L | 1.554 | 1.00 |
| 371_Q | 379_E | 1.553 | 1.00 |
| 677_L | 690_Q | 1.553 | 1.00 |
| 418_M | 422_E | 1.550 | 1.00 |
| 726_K | 729_K | 1.547 | 1.00 |
| 132_N | 140_K | 1.544 | 1.00 |
| 175_E | 279_L | 1.530 | 1.00 |
| 736_N | 745_L | 1.529 | 1.00 |
| 453_D | 456_R | 1.525 | 1.00 |
| 436_N | 440_E | 1.525 | 1.00 |
| 26_N | 63_L | 1.522 | 1.00 |
| 748_D | 751_A | 1.521 | 1.00 |
| 458_S | 461_Q | 1.520 | 1.00 |
| 647_D | 770_K | 1.518 | 1.00 |
| 300_Y | 621_R | 1.516 | 1.00 |
| 408_Q | 412_E | 1.516 | 1.00 |
| 437_K | 464_V | 1.506 | 1.00 |
| 141_Q | 144_K | 1.499 | 1.00 |
| 190_R | 194_D | 1.497 | 1.00 |
| 514_L | 533_S | 1.494 | 1.00 |
| 440_E | 444_K | 1.489 | 1.00 |
| 531_A | 714_I | 1.488 | 1.00 |
| 537_L | 783_K | 1.488 | 1.00 |
| 776_A | 780_D | 1.487 | 1.00 |
| 137_D | 204_I | 1.485 | 1.00 |
| 754_K | 776_A | 1.485 | 1.00 |
| 519_S | 529_I | 1.485 | 1.00 |
| 759_A | 769_L | 1.484 | 1.00 |
| 743_I | 790_I | 1.483 | 1.00 |
| 758_D | 772_Y | 1.479 | 1.00 |
| 574_L | 665_V | 1.473 | 0.99 |
| 582_V | 618_V | 1.472 | 0.99 |
| 333_L | 357_V | 1.471 | 0.99 |
| 10_V | 103_V | 1.467 | 0.99 |
| 83_I | 107_M | 1.458 | 0.99 |
| 309_T | 349_L | 1.458 | 0.99 |
| 697_V | 700_S | 1.446 | 0.99 |
| 317_K | 330_D | 1.446 | 0.99 |
| 129_D | 231_E | 1.442 | 0.99 |
| 225_L | 228_V | 1.432 | 0.99 |
| 512_I | 787_A | 1.431 | 0.99 |
| 441_T | 468_L | 1.427 | 0.99 |
| 34_L | 80_L | 1.424 | 0.99 |
| 316_L | 319_R | 1.423 | 0.99 |
| 229_M | 265_M | 1.421 | 0.99 |
| 379_E | 418_M | 1.420 | 0.99 |
| 385_L | 403_V | 1.417 | 0.99 |
| 189_N | 193_Q | 1.417 | 0.99 |
| 318_D | 322_R | 1.414 | 0.99 |
| 412_E | 416_P | 1.403 | 0.99 |
| 148_V | 155_I | 1.396 | 0.99 |
| 327_R | 482_E | 1.391 | 0.99 |
| 437_K | 440_E | 1.389 | 0.99 |
| 329_D | 332_A | 1.382 | 0.99 |
| 303_E | 341_H | 1.380 | 0.99 |
| 363_N | 490_H | 1.369 | 0.99 |
| 518_L | 569_K | 1.367 | 0.99 |
| 459_D | 464_V | 1.366 | 0.99 |
| 412_E | 415_K | 1.357 | 0.99 |
| 676_I | 697_V | 1.356 | 0.99 |
| 422_E | 426_E | 1.352 | 0.99 |
| 442_Q | 469_E | 1.352 | 0.99 |
| 642_F | 645_V | 1.352 | 0.99 |
| 464_V | 467_D | 1.349 | 0.99 |
| 539_S | 544_S | 1.341 | 0.99 |
| 340_S | 352_K | 1.335 | 0.99 |
| 518_L | 522_V | 1.335 | 0.99 |
| 584_I | 598_L | 1.320 | 0.99 |
| 331_S | 485_A | 1.311 | 0.99 |
| 246_M | 275_G | 1.309 | 0.99 |
| 20_L | 37_S | 1.308 | 0.99 |
| 532_V | 566_L | 1.307 | 0.99 |
| 360_A | 488_I | 1.306 | 0.98 |
| 20_L | 23_A | 1.301 | 0.98 |
| 554_L | 698_I | 1.300 | 0.98 |
| 759_A | 772_Y | 1.298 | 0.98 |
| 590_M | 637_D | 1.296 | 0.98 |
| 157_R | 359_E | 1.294 | 0.98 |
| 784_R | 787_A | 1.288 | 0.98 |
| 742_N | 792_P | 1.284 | 0.98 |
| 601_A | 628_L | 1.281 | 0.98 |
| 308_D | 311_S | 1.280 | 0.98 |
| 310_V | 337_A | 1.279 | 0.98 |
| 445_I | 465_L | 1.279 | 0.98 |
| 595_V | 641_L | 1.279 | 0.98 |
| 232_V | 241_L | 1.277 | 0.98 |
| 729_K | 749_D | 1.276 | 0.98 |
| 438_V | 468_L | 1.271 | 0.98 |
| 581_I | 625_V | 1.271 | 0.98 |
| 738_R | 778_V | 1.270 | 0.98 |
| 589_Y | 613_E | 1.268 | 0.98 |
| 548_K | 770_K | 1.268 | 0.98 |
| 515_P | 533_S | 1.268 | 0.98 |
| 687_C | 690_Q | 1.268 | 0.98 |
| 554_L | 631_V | 1.267 | 0.98 |
| 628_L | 645_V | 1.267 | 0.98 |
| 791_M | 794_F | 1.266 | 0.98 |
| 9_Y | 12_E | 1.252 | 0.98 |
| 723_Q | 726_K | 1.248 | 0.98 |
| 691_K | 695_M | 1.247 | 0.98 |
| 721_Y | 756_M | 1.247 | 0.98 |
| 433_R | 436_N | 1.245 | 0.98 |
| 748_D | 797_L | 1.244 | 0.98 |
| 455_A | 458_S | 1.243 | 0.98 |
| 529_I | 532_V | 1.242 | 0.98 |
| 784_R | 790_I | 1.236 | 0.98 |
| 619_R | 657_R | 1.233 | 0.98 |
| 349_L | 353_A | 1.229 | 0.98 |
| 381_K | 406_E | 1.227 | 0.97 |
| 487_D | 490_H | 1.226 | 0.97 |
| 13_N | 41_D | 1.223 | 0.97 |
| 506_S | 509_D | 1.222 | 0.97 |
| 728_M | 773_I | 1.219 | 0.97 |
| 597_R | 654_K | 1.210 | 0.97 |
| 468_L | 471_A | 1.207 | 0.97 |
| 750_S | 753_E | 1.203 | 0.97 |
| 13_N | 38_M | 1.203 | 0.97 |
| 283_K | 655_Q | 1.202 | 0.97 |
| 695_M | 715_M | 1.198 | 0.97 |
| 173_I | 298_Q | 1.197 | 0.97 |
| 31_N | 83_I | 1.196 | 0.97 |
| 743_I | 785_L | 1.195 | 0.97 |
| 722_E | 725_K | 1.194 | 0.97 |
| 724_M | 760_Y | 1.187 | 0.97 |
| 596_S | 599_V | 1.183 | 0.97 |
| 414_L | 418_M | 1.178 | 0.97 |
| 191_I | 203_L | 1.177 | 0.97 |
| 777_I | 798_S | 1.177 | 0.97 |
| 780_D | 784_R | 1.177 | 0.97 |
| 441_T | 464_V | 1.173 | 0.96 |
| 692_Q | 696_Q | 1.172 | 0.96 |
| 628_L | 668_M | 1.169 | 0.96 |
| 675_D | 697_V | 1.169 | 0.96 |
| 62_Q | 65_K | 1.165 | 0.96 |
| 675_D | 679_Q | 1.164 | 0.96 |
| 157_R | 160_R | 1.163 | 0.96 |
| 781_L | 796_S | 1.161 | 0.96 |
| 30_S | 77_S | 1.160 | 0.96 |
| 27_P | 69_Q | 1.155 | 0.96 |
| 283_K | 616_E | 1.153 | 0.96 |
| 595_V | 638_V | 1.150 | 0.96 |
| 520_E | 733_D | 1.147 | 0.96 |
| 590_M | 640_N | 1.145 | 0.96 |
| 208_L | 249_L | 1.145 | 0.96 |
| 519_S | 530_E | 1.140 | 0.96 |
| 591_E | 602_P | 1.140 | 0.96 |
| 538_R | 779_T | 1.133 | 0.95 |
| 773_I | 777_I | 1.131 | 0.95 |
| 702_F | 706_F | 1.129 | 0.95 |
| 734_E | 737_N | 1.128 | 0.95 |
| 512_I | 783_K | 1.128 | 0.95 |
| 735_L | 778_V | 1.127 | 0.95 |
| 365_R | 369_D | 1.123 | 0.95 |
| 26_N | 33_H | 1.122 | 0.95 |
| 761_D | 768_P | 1.117 | 0.95 |
| 469_E | 473_Q | 1.113 | 0.95 |
| 76_F | 80_L | 1.110 | 0.95 |
| 599_V | 641_L | 1.109 | 0.95 |
| 155_I | 186_G | 1.105 | 0.95 |
| 44_P | 104_L | 1.104 | 0.95 |
| 189_N | 192_V | 1.104 | 0.95 |
| 335_L | 338_K | 1.103 | 0.95 |
| 164_R | 169_N | 1.103 | 0.95 |
| 24_N | 64_K | 1.103 | 0.95 |
| 569_K | 572_L | 1.103 | 0.95 |
| 441_T | 445_I | 1.100 | 0.94 |
| 584_I | 597_R | 1.098 | 0.94 |
| 139_V | 192_V | 1.094 | 0.94 |
| 732_I | 736_N | 1.093 | 0.94 |
| 544_S | 550_T | 1.093 | 0.94 |
| 445_I | 461_Q | 1.091 | 0.94 |
| 32_V | 36_V | 1.090 | 0.94 |
| 249_L | 259_A | 1.090 | 0.94 |
| 511_L | 540_R | 1.086 | 0.94 |
| 584_I | 628_L | 1.084 | 0.94 |
| 753_E | 757_K | 1.080 | 0.94 |
| 545_R | 734_E | 1.076 | 0.94 |
| 592_K | 597_R | 1.075 | 0.94 |
| 31_N | 80_L | 1.074 | 0.93 |
| 690_Q | 717_N | 1.072 | 0.93 |
| 437_K | 471_A | 1.071 | 0.93 |
| 322_R | 325_G | 1.071 | 0.93 |
| 88_Q | 98_V | 1.069 | 0.93 |
| 379_E | 414_L | 1.068 | 0.93 |
| 306_V | 309_T | 1.067 | 0.93 |
| 519_S | 717_N | 1.067 | 0.93 |
| 490_H | 501_D | 1.065 | 0.93 |
| 215_A | 228_V | 1.064 | 0.93 |
| 158_V | 172_L | 1.062 | 0.93 |
| 744_A | 795_Y | 1.060 | 0.93 |
| 444_K | 447_A | 1.059 | 0.93 |
| 725_K | 729_K | 1.057 | 0.93 |
| 314_R | 334_V | 1.056 | 0.93 |
| 608_Y | 654_K | 1.055 | 0.93 |
| 340_S | 356_L | 1.051 | 0.92 |
| 32_V | 79_S | 1.050 | 0.92 |
| 420_R | 424_E | 1.048 | 0.92 |
| 94_Q | 110_F | 1.044 | 0.92 |
| 537_L | 779_T | 1.043 | 0.92 |
| 323_Y | 365_R | 1.043 | 0.92 |
| 388_E | 399_R | 1.042 | 0.92 |
| 448_A | 457_A | 1.040 | 0.92 |
| 618_V | 626_I | 1.039 | 0.92 |
| 381_K | 384_Q | 1.039 | 0.92 |
| 706_F | 710_L | 1.038 | 0.92 |
| 145_I | 148_V | 1.038 | 0.92 |
| 183_I | 301_V | 1.038 | 0.92 |
| 87_A | 103_V | 1.035 | 0.92 |
| 373_E | 378_L | 1.028 | 0.91 |
| 329_D | 482_E | 1.027 | 0.91 |
| 438_V | 442_Q | 1.025 | 0.91 |
| 389_Q | 400_L | 1.025 | 0.91 |
| 729_K | 733_D | 1.024 | 0.91 |
| 21_A | 33_H | 1.024 | 0.91 |
| 110_F | 113_G | 1.024 | 0.91 |
| 329_D | 484_T | 1.024 | 0.91 |
| 684_T | 687_C | 1.022 | 0.91 |
| 90_N | 106_A | 1.021 | 0.91 |
| 746_E | 795_Y | 1.021 | 0.91 |
| 749_D | 753_E | 1.021 | 0.91 |
| 20_L | 24_N | 1.016 | 0.91 |
| 158_V | 184_V | 1.016 | 0.91 |
| 530_E | 534_N | 1.015 | 0.91 |
| 310_V | 338_K | 1.014 | 0.91 |
| 163_C | 198_T | 1.014 | 0.91 |
| 751_A | 777_I | 1.010 | 0.90 |
| 790_I | 794_F | 1.008 | 0.90 |
| 251_G | 257_D | 1.008 | 0.90 |
| 755_I | 759_A | 1.007 | 0.90 |
| 371_Q | 418_M | 1.005 | 0.90 |
| 538_R | 778_V | 1.005 | 0.90 |
| 374_E | 413_Q | 1.002 | 0.90 |
| 712_E | 775_R | 1.002 | 0.90 |
| 6_F | 10_V | 1.001 | 0.90 |
| 206_L | 211_L | 1.000 | 0.90 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 1qvrA | 3 | 0.9425 | 100 | 0.417 | Contact Map |
| 4d2uA | 6 | 0.9325 | 100 | 0.426 | Contact Map |
| 1r6bX | 1 | 0.8163 | 100 | 0.436 | Contact Map |
| 3pxiA | 3 | 0.835 | 100 | 0.475 | Contact Map |
| 4ciuA | 1 | 0.7937 | 100 | 0.536 | Contact Map |
| 3vkgA | 2 | 0.8475 | 100 | 0.738 | Contact Map |
| 3pxgA | 6 | 0.515 | 100 | 0.752 | Contact Map |
| 4lj9A | 1 | 0.4012 | 100 | 0.781 | Contact Map |
| 4hseA | 1 | 0.4475 | 100 | 0.796 | Contact Map |
| 4akgA | 2 | 0.8125 | 100 | 0.816 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)