| 740-1721 |
| ID: | 1460555998 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 982 (416) | ||
| Sequences: | 4452 (2327.1) | ||
| Seq/Len: | 10.702 | ||
| Nf(neff/√len): | 114.1 |
HHblits Results: (2015_06)
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: 10.702).
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 |
| 563_R | 578_D | 4.380 | 1.00 |
| 511_E | 561_R | 3.996 | 1.00 |
| 683_E | 686_R | 3.333 | 1.00 |
| 726_H | 826_K | 2.859 | 1.00 |
| 741_G | 750_L | 2.778 | 1.00 |
| 722_R | 746_D | 2.662 | 1.00 |
| 730_L | 741_G | 2.635 | 1.00 |
| 638_K | 645_R | 2.546 | 1.00 |
| 502_Y | 653_I | 2.485 | 1.00 |
| 516_D | 638_K | 2.462 | 1.00 |
| 499_R | 657_T | 2.451 | 1.00 |
| 644_T | 647_P | 2.273 | 1.00 |
| 505_E | 509_T | 2.246 | 1.00 |
| 506_L | 653_I | 2.241 | 1.00 |
| 518_Q | 554_I | 2.238 | 1.00 |
| 730_L | 814_A | 2.229 | 1.00 |
| 509_T | 642_R | 2.221 | 1.00 |
| 513_Y | 590_Y | 2.178 | 1.00 |
| 742_F | 751_T | 2.165 | 1.00 |
| 741_G | 748_L | 2.139 | 1.00 |
| 559_A | 582_A | 2.105 | 1.00 |
| 645_R | 648_L | 2.087 | 1.00 |
| 642_R | 646_Y | 2.057 | 1.00 |
| 651_K | 675_E | 2.006 | 1.00 |
| 743_L | 823_W | 1.996 | 1.00 |
| 647_P | 651_K | 1.989 | 1.00 |
| 743_L | 748_L | 1.975 | 1.00 |
| 513_Y | 517_L | 1.945 | 1.00 |
| 659_E | 664_H | 1.918 | 1.00 |
| 593_F | 639_P | 1.917 | 1.00 |
| 535_T | 538_E | 1.870 | 1.00 |
| 657_T | 667_L | 1.823 | 1.00 |
| 652_N | 655_E | 1.808 | 1.00 |
| 641_Q | 648_L | 1.807 | 1.00 |
| 514_V | 553_N | 1.804 | 1.00 |
| 614_F | 618_V | 1.803 | 1.00 |
| 647_P | 675_E | 1.798 | 1.00 |
| 505_E | 510_E | 1.795 | 1.00 |
| 648_L | 682_N | 1.778 | 1.00 |
| 637_L | 641_Q | 1.769 | 1.00 |
| 693_R | 727_S | 1.733 | 1.00 |
| 525_Q | 529_M | 1.721 | 1.00 |
| 524_F | 627_C | 1.707 | 1.00 |
| 685_V | 689_E | 1.690 | 1.00 |
| 559_A | 583_Q | 1.680 | 1.00 |
| 556_L | 560_L | 1.677 | 1.00 |
| 650_I | 667_L | 1.656 | 1.00 |
| 790_L | 820_R | 1.654 | 1.00 |
| 722_R | 745_N | 1.650 | 1.00 |
| 654_L | 667_L | 1.610 | 1.00 |
| 825_Q | 829_A | 1.599 | 1.00 |
| 728_G | 823_W | 1.565 | 1.00 |
| 518_Q | 550_I | 1.543 | 1.00 |
| 617_F | 621_L | 1.540 | 1.00 |
| 741_G | 812_L | 1.533 | 1.00 |
| 637_L | 640_M | 1.528 | 1.00 |
| 644_T | 678_C | 1.527 | 1.00 |
| 650_I | 674_A | 1.521 | 1.00 |
| 631_P | 634_S | 1.513 | 1.00 |
| 597_Q | 601_A | 1.507 | 1.00 |
| 519_L | 524_F | 1.499 | 1.00 |
| 502_Y | 652_N | 1.496 | 1.00 |
| 557_L | 561_R | 1.489 | 1.00 |
| 635_F | 639_P | 1.489 | 1.00 |
| 594_C | 647_P | 1.484 | 1.00 |
| 642_R | 649_I | 1.480 | 1.00 |
| 596_R | 600_G | 1.472 | 1.00 |
| 671_L | 675_E | 1.472 | 1.00 |
| 725_L | 830_A | 1.471 | 1.00 |
| 563_R | 579_I | 1.465 | 1.00 |
| 642_R | 648_L | 1.464 | 1.00 |
| 686_R | 689_E | 1.453 | 1.00 |
| 641_Q | 644_T | 1.446 | 1.00 |
| 544_V | 596_R | 1.433 | 1.00 |
| 510_E | 517_L | 1.430 | 1.00 |
| 505_E | 648_L | 1.422 | 1.00 |
| 801_F | 814_A | 1.417 | 1.00 |
| 684_G | 687_E | 1.415 | 1.00 |
| 510_E | 513_Y | 1.415 | 1.00 |
| 816_S | 819_E | 1.405 | 0.99 |
| 654_L | 671_L | 1.403 | 0.99 |
| 521_T | 550_I | 1.402 | 0.99 |
| 514_V | 557_L | 1.400 | 0.99 |
| 545_N | 548_E | 1.390 | 0.99 |
| 525_Q | 547_K | 1.374 | 0.99 |
| 503_I | 507_I | 1.366 | 0.99 |
| 506_L | 580_L | 1.364 | 0.99 |
| 658_P | 661_H | 1.361 | 0.99 |
| 522_E | 526_K | 1.358 | 0.99 |
| 594_C | 644_T | 1.348 | 0.99 |
| 512_N | 516_D | 1.338 | 0.99 |
| 575_M | 666_H | 1.336 | 0.99 |
| 437_F | 443_I | 1.334 | 0.99 |
| 640_M | 644_T | 1.328 | 0.99 |
| 643_V | 681_V | 1.324 | 0.99 |
| 505_E | 513_Y | 1.319 | 0.99 |
| 668_K | 672_E | 1.316 | 0.99 |
| 801_F | 824_V | 1.313 | 0.99 |
| 593_F | 596_R | 1.305 | 0.99 |
| 520_V | 546_W | 1.302 | 0.99 |
| 732_K | 750_L | 1.301 | 0.99 |
| 664_H | 668_K | 1.299 | 0.99 |
| 641_Q | 682_N | 1.297 | 0.99 |
| 577_G | 663_D | 1.294 | 0.99 |
| 509_T | 513_Y | 1.287 | 0.99 |
| 728_G | 740_Y | 1.286 | 0.99 |
| 456_G | 465_F | 1.286 | 0.99 |
| 642_R | 645_R | 1.274 | 0.99 |
| 504_H | 508_V | 1.274 | 0.99 |
| 727_S | 740_Y | 1.272 | 0.99 |
| 516_D | 628_K | 1.270 | 0.99 |
| 814_A | 823_W | 1.258 | 0.99 |
| 826_K | 829_A | 1.241 | 0.98 |
| 596_R | 599_N | 1.235 | 0.98 |
| 666_H | 669_H | 1.229 | 0.98 |
| 636_I | 639_P | 1.223 | 0.98 |
| 634_S | 637_L | 1.218 | 0.98 |
| 542_I | 604_I | 1.218 | 0.98 |
| 724_F | 742_F | 1.218 | 0.98 |
| 506_L | 510_E | 1.216 | 0.98 |
| 687_E | 723_K | 1.215 | 0.98 |
| 519_L | 627_C | 1.214 | 0.98 |
| 639_P | 642_R | 1.214 | 0.98 |
| 641_Q | 649_I | 1.210 | 0.98 |
| 823_W | 827_I | 1.208 | 0.98 |
| 505_E | 649_I | 1.205 | 0.98 |
| 645_R | 678_C | 1.198 | 0.98 |
| 726_H | 730_L | 1.198 | 0.98 |
| 538_E | 607_K | 1.197 | 0.98 |
| 641_Q | 645_R | 1.190 | 0.98 |
| 750_L | 812_L | 1.187 | 0.98 |
| 546_W | 550_I | 1.176 | 0.98 |
| 577_G | 667_L | 1.173 | 0.98 |
| 465_F | 470_V | 1.161 | 0.97 |
| 731_Y | 738_E | 1.161 | 0.97 |
| 597_Q | 640_M | 1.161 | 0.97 |
| 645_R | 649_I | 1.159 | 0.97 |
| 644_T | 648_L | 1.154 | 0.97 |
| 777_Y | 780_P | 1.151 | 0.97 |
| 527_P | 617_F | 1.148 | 0.97 |
| 632_L | 639_P | 1.146 | 0.97 |
| 632_L | 636_I | 1.144 | 0.97 |
| 640_M | 648_L | 1.140 | 0.97 |
| 520_V | 632_L | 1.138 | 0.97 |
| 526_K | 530_E | 1.135 | 0.97 |
| 524_F | 622_A | 1.134 | 0.97 |
| 726_H | 822_A | 1.132 | 0.97 |
| 591_I | 595_S | 1.128 | 0.97 |
| 591_I | 680_Q | 1.126 | 0.97 |
| 739_L | 750_L | 1.124 | 0.97 |
| 653_I | 657_T | 1.123 | 0.97 |
| 509_T | 512_N | 1.122 | 0.97 |
| 577_G | 670_A | 1.113 | 0.96 |
| 580_L | 650_I | 1.110 | 0.96 |
| 482_W | 486_L | 1.106 | 0.96 |
| 590_Y | 593_F | 1.103 | 0.96 |
| 663_D | 666_H | 1.097 | 0.96 |
| 529_M | 539_V | 1.088 | 0.96 |
| 506_L | 649_I | 1.085 | 0.96 |
| 550_I | 554_I | 1.084 | 0.96 |
| 719_L | 722_R | 1.083 | 0.96 |
| 505_E | 517_L | 1.082 | 0.96 |
| 783_L | 786_V | 1.079 | 0.95 |
| 814_A | 820_R | 1.078 | 0.95 |
| 499_R | 661_H | 1.077 | 0.95 |
| 824_V | 828_K | 1.077 | 0.95 |
| 501_G | 504_H | 1.065 | 0.95 |
| 740_Y | 751_T | 1.063 | 0.95 |
| 505_E | 645_R | 1.058 | 0.95 |
| 639_P | 646_Y | 1.056 | 0.95 |
| 646_Y | 649_I | 1.053 | 0.95 |
| 594_C | 645_R | 1.053 | 0.95 |
| 508_V | 512_N | 1.045 | 0.94 |
| 580_L | 646_Y | 1.041 | 0.94 |
| 529_M | 547_K | 1.034 | 0.94 |
| 786_V | 806_I | 1.032 | 0.94 |
| 553_N | 556_L | 1.032 | 0.94 |
| 682_N | 686_R | 1.029 | 0.94 |
| 638_K | 644_T | 1.027 | 0.94 |
| 502_Y | 580_L | 1.027 | 0.94 |
| 505_E | 682_N | 1.020 | 0.93 |
| 594_C | 597_Q | 1.012 | 0.93 |
| 519_L | 523_I | 1.011 | 0.93 |
| 820_R | 824_V | 1.009 | 0.93 |
| 665_S | 668_K | 1.007 | 0.93 |
| 581_S | 669_H | 1.007 | 0.93 |
| 639_P | 643_V | 1.004 | 0.93 |
| 597_Q | 644_T | 1.003 | 0.93 |
| 630_M | 634_S | 1.001 | 0.92 |
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 | |
| 3jzyA | 1 | 0.1263 | 100 | 0.608 | Contact Map |
| 4mt7A | 1 | 0.3269 | 100 | 0.688 | Contact Map |
| 2pz1A | 1 | 0.4022 | 100 | 0.693 | Contact Map |
| 4xh9A | 2 | 0.335 | 100 | 0.738 | Contact Map |
| 3jv3A | 2 | 0.2841 | 100 | 0.739 | Contact Map |
| 2z0qA | 1 | 0.3096 | 100 | 0.743 | Contact Map |
| 1xcgA | 2 | 0.3411 | 100 | 0.748 | Contact Map |
| 4yonA | 1 | 0 | 100 | 0.748 | Contact Map |
| 3ksyA | 1 | 0.6161 | 100 | 0.75 | Contact Map |
| 3odwA | 2 | 0.3248 | 100 | 0.751 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)