| cftr full |
| ID: | 1488225967 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 644 (515) | ||
| Sequences: | 8346 (5607.3) | ||
| Seq/Len: | 16.206 | ||
| Nf(neff/√len): | 247.1 |
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: 16.206).
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 |
| 422_D | 437_N | 6.368 | 1.00 |
| 419_T | 441_S | 5.368 | 1.00 |
| 446_Q | 620_Q | 5.029 | 1.00 |
| 421_K | 474_E | 4.963 | 1.00 |
| 533_R | 543_L | 4.950 | 1.00 |
| 443_S | 446_Q | 4.804 | 1.00 |
| 474_E | 481_S | 4.533 | 1.00 |
| 417_Q | 441_S | 4.408 | 1.00 |
| 633_D | 637_K | 4.338 | 1.00 |
| 528_D | 533_R | 4.153 | 1.00 |
| 620_Q | 632_Y | 4.085 | 1.00 |
| 436_E | 628_K | 4.067 | 1.00 |
| 420_V | 423_L | 4.026 | 1.00 |
| 421_K | 476_Q | 3.828 | 1.00 |
| 519_S | 522_E | 3.692 | 1.00 |
| 440_F | 622_L | 3.613 | 1.00 |
| 424_T | 437_N | 3.576 | 1.00 |
| 509_R | 520_D | 3.556 | 1.00 |
| 533_R | 537_E | 3.442 | 1.00 |
| 506_G | 510_K | 3.295 | 1.00 |
| 509_R | 544_D | 3.136 | 1.00 |
| 419_T | 476_Q | 3.062 | 1.00 |
| 527_A | 543_L | 2.949 | 1.00 |
| 417_Q | 443_S | 2.926 | 1.00 |
| 416_G | 478_D | 2.889 | 1.00 |
| 512_L | 527_A | 2.794 | 1.00 |
| 524_W | 528_D | 2.760 | 1.00 |
| 512_L | 523_I | 2.672 | 1.00 |
| 509_R | 523_I | 2.649 | 1.00 |
| 214_A | 218_V | 2.628 | 1.00 |
| 634_S | 637_K | 2.627 | 1.00 |
| 597_K | 617_E | 2.605 | 1.00 |
| 424_T | 433_A | 2.569 | 1.00 |
| 509_R | 513_D | 2.533 | 1.00 |
| 495_G | 572_A | 2.531 | 1.00 |
| 417_Q | 444_P | 2.470 | 1.00 |
| 435_L | 438_I | 2.467 | 1.00 |
| 525_K | 529_E | 2.435 | 1.00 |
| 418_M | 606_I | 2.382 | 1.00 |
| 462_L | 576_L | 2.377 | 1.00 |
| 524_W | 533_R | 2.350 | 1.00 |
| 462_L | 608_C | 2.338 | 1.00 |
| 420_V | 440_F | 2.336 | 1.00 |
| 278_R | 281_Y | 2.282 | 1.00 |
| 486_T | 489_Q | 2.260 | 1.00 |
| 481_S | 484_S | 2.259 | 1.00 |
| 520_D | 524_W | 2.248 | 1.00 |
| 571_K | 603_C | 2.247 | 1.00 |
| 450_L | 461_L | 2.225 | 1.00 |
| 217_A | 224_F | 2.191 | 1.00 |
| 467_R | 470_N | 2.157 | 1.00 |
| 622_L | 632_Y | 2.140 | 1.00 |
| 442_I | 606_I | 2.128 | 1.00 |
| 609_E | 614_A | 2.124 | 1.00 |
| 433_A | 436_E | 2.122 | 1.00 |
| 470_N | 483_D | 2.107 | 1.00 |
| 448_V | 620_Q | 2.106 | 1.00 |
| 631_Q | 641_E | 2.089 | 1.00 |
| 541_G | 545_F | 2.074 | 1.00 |
| 426_K | 472_E | 2.046 | 1.00 |
| 422_D | 439_S | 2.025 | 1.00 |
| 547_L | 554_L | 2.015 | 1.00 |
| 631_Q | 642_R | 2.003 | 1.00 |
| 513_D | 520_D | 1.991 | 1.00 |
| 524_W | 543_L | 1.973 | 1.00 |
| 426_K | 433_A | 1.972 | 1.00 |
| 415_G | 478_D | 1.965 | 1.00 |
| 526_V | 530_V | 1.958 | 1.00 |
| 532_L | 535_V | 1.952 | 1.00 |
| 464_A | 475_I | 1.950 | 1.00 |
| 442_I | 448_V | 1.920 | 1.00 |
| 525_K | 528_D | 1.899 | 1.00 |
| 372_F | 376_D | 1.897 | 1.00 |
| 590_Q | 594_R | 1.897 | 1.00 |
| 527_A | 536_I | 1.890 | 1.00 |
| 447_R | 618_C | 1.889 | 1.00 |
| 513_D | 523_I | 1.862 | 1.00 |
| 524_W | 537_E | 1.854 | 1.00 |
| 493_A | 573_K | 1.840 | 1.00 |
| 522_E | 571_K | 1.840 | 1.00 |
| 447_R | 607_L | 1.806 | 1.00 |
| 508_F | 562_M | 1.758 | 1.00 |
| 622_L | 629_V | 1.741 | 1.00 |
| 594_R | 598_Q | 1.721 | 1.00 |
| 417_Q | 478_D | 1.719 | 1.00 |
| 437_N | 628_K | 1.704 | 1.00 |
| 285_L | 289_A | 1.695 | 1.00 |
| 163_S | 379_T | 1.658 | 1.00 |
| 250_Q | 369_S | 1.655 | 1.00 |
| 621_F | 635_I | 1.646 | 1.00 |
| 187_D | 370_R | 1.645 | 1.00 |
| 471_T | 482_W | 1.638 | 1.00 |
| 454_T | 588_T | 1.636 | 1.00 |
| 521_Q | 524_W | 1.631 | 1.00 |
| 475_I | 482_W | 1.592 | 1.00 |
| 423_L | 471_T | 1.577 | 1.00 |
| 438_I | 629_V | 1.540 | 1.00 |
| 631_Q | 638_L | 1.534 | 1.00 |
| 477_I | 574_I | 1.531 | 1.00 |
| 383_P | 486_T | 1.517 | 1.00 |
| 449_G | 618_C | 1.517 | 1.00 |
| 631_Q | 643_S | 1.509 | 1.00 |
| 548_V | 553_V | 1.501 | 1.00 |
| 607_L | 618_C | 1.499 | 1.00 |
| 418_M | 477_I | 1.493 | 1.00 |
| 624_I | 629_V | 1.490 | 1.00 |
| 466_L | 496_V | 1.478 | 1.00 |
| 425_A | 469_L | 1.471 | 1.00 |
| 440_F | 461_L | 1.468 | 1.00 |
| 529_E | 568_V | 1.466 | 1.00 |
| 191_L | 371_V | 1.461 | 1.00 |
| 535_V | 558_H | 1.452 | 1.00 |
| 495_G | 567_S | 1.444 | 1.00 |
| 176_K | 179_G | 1.444 | 1.00 |
| 534_S | 537_E | 1.444 | 1.00 |
| 443_S | 620_Q | 1.442 | 1.00 |
| 522_E | 525_K | 1.430 | 1.00 |
| 166_Q | 379_T | 1.426 | 1.00 |
| 518_W | 569_L | 1.421 | 1.00 |
| 461_L | 624_I | 1.414 | 1.00 |
| 223_I | 340_I | 1.391 | 0.99 |
| 637_K | 641_E | 1.388 | 0.99 |
| 418_M | 442_I | 1.381 | 0.99 |
| 527_A | 533_R | 1.379 | 0.99 |
| 466_L | 494_F | 1.378 | 0.99 |
| 255_G | 292_L | 1.376 | 0.99 |
| 532_L | 536_I | 1.365 | 0.99 |
| 482_W | 490_W | 1.354 | 0.99 |
| 217_A | 221_P | 1.350 | 0.99 |
| 419_T | 439_S | 1.344 | 0.99 |
| 633_D | 638_L | 1.342 | 0.99 |
| 471_T | 483_D | 1.335 | 0.99 |
| 173_N | 463_S | 1.335 | 0.99 |
| 467_R | 487_L | 1.330 | 0.99 |
| 527_A | 532_L | 1.321 | 0.99 |
| 262_H | 289_A | 1.320 | 0.99 |
| 509_R | 543_L | 1.316 | 0.99 |
| 625_E | 630_R | 1.315 | 0.99 |
| 448_V | 622_L | 1.313 | 0.99 |
| 446_Q | 632_Y | 1.311 | 0.99 |
| 529_E | 598_Q | 1.306 | 0.99 |
| 414_S | 478_D | 1.304 | 0.99 |
| 450_L | 622_L | 1.302 | 0.99 |
| 428_T | 431_G | 1.300 | 0.99 |
| 269_G | 502_F | 1.299 | 0.99 |
| 425_A | 460_T | 1.292 | 0.99 |
| 518_W | 522_E | 1.286 | 0.99 |
| 616_L | 636_Q | 1.274 | 0.99 |
| 480_V | 485_I | 1.267 | 0.99 |
| 636_Q | 640_N | 1.264 | 0.99 |
| 421_K | 439_S | 1.263 | 0.99 |
| 446_Q | 619_Q | 1.263 | 0.99 |
| 449_G | 615_M | 1.261 | 0.99 |
| 440_F | 629_V | 1.260 | 0.99 |
| 524_W | 527_A | 1.256 | 0.99 |
| 168_P | 380_E | 1.252 | 0.99 |
| 522_E | 569_L | 1.219 | 0.98 |
| 420_V | 465_F | 1.218 | 0.98 |
| 584_L | 592_I | 1.218 | 0.98 |
| 635_I | 639_L | 1.215 | 0.98 |
| 564_L | 577_L | 1.208 | 0.98 |
| 531_G | 591_I | 1.208 | 0.98 |
| 520_D | 523_I | 1.206 | 0.98 |
| 589_Y | 611_R | 1.206 | 0.98 |
| 536_I | 543_L | 1.203 | 0.98 |
| 447_R | 605_V | 1.197 | 0.98 |
| 438_I | 461_L | 1.194 | 0.98 |
| 529_E | 599_A | 1.182 | 0.98 |
| 163_S | 167_A | 1.179 | 0.98 |
| 419_T | 479_G | 1.179 | 0.98 |
| 453_R | 625_E | 1.178 | 0.98 |
| 535_V | 539_F | 1.175 | 0.98 |
| 306_W | 310_R | 1.169 | 0.97 |
| 132_D | 136_A | 1.167 | 0.97 |
| 635_I | 638_L | 1.162 | 0.97 |
| 548_V | 552_C | 1.160 | 0.97 |
| 623_V | 638_L | 1.160 | 0.97 |
| 556_H | 561_L | 1.158 | 0.97 |
| 286_F | 290_L | 1.155 | 0.97 |
| 505_S | 546_V | 1.155 | 0.97 |
| 183_R | 373_K | 1.149 | 0.97 |
| 255_G | 293_H | 1.144 | 0.97 |
| 609_E | 615_M | 1.144 | 0.97 |
| 531_G | 588_T | 1.140 | 0.97 |
| 447_R | 602_D | 1.138 | 0.97 |
| 454_T | 561_L | 1.130 | 0.97 |
| 525_K | 571_K | 1.121 | 0.97 |
| 637_K | 640_N | 1.118 | 0.96 |
| 465_F | 606_I | 1.117 | 0.96 |
| 530_V | 565_A | 1.099 | 0.96 |
| 530_V | 561_L | 1.090 | 0.96 |
| 222_Y | 225_V | 1.084 | 0.96 |
| 507_T | 510_K | 1.083 | 0.96 |
| 221_P | 225_V | 1.081 | 0.95 |
| 485_I | 489_Q | 1.079 | 0.95 |
| 416_G | 444_P | 1.077 | 0.95 |
| 384_T | 484_S | 1.072 | 0.95 |
| 485_I | 490_W | 1.067 | 0.95 |
| 623_V | 631_Q | 1.065 | 0.95 |
| 190_I | 367_S | 1.065 | 0.95 |
| 579_E | 610_H | 1.063 | 0.95 |
| 537_E | 542_K | 1.063 | 0.95 |
| 381_G | 470_N | 1.063 | 0.95 |
| 611_R | 614_A | 1.062 | 0.95 |
| 415_G | 444_P | 1.061 | 0.95 |
| 187_D | 367_S | 1.060 | 0.95 |
| 425_A | 464_A | 1.055 | 0.95 |
| 160_M | 374_F | 1.052 | 0.95 |
| 163_S | 375_I | 1.044 | 0.94 |
| 444_P | 478_D | 1.040 | 0.94 |
| 162_H | 166_Q | 1.023 | 0.93 |
| 532_L | 562_M | 1.022 | 0.93 |
| 521_Q | 525_K | 1.021 | 0.93 |
| 492_K | 570_S | 1.020 | 0.93 |
| 532_L | 543_L | 1.014 | 0.93 |
| 284_T | 288_K | 1.012 | 0.93 |
| 512_L | 562_M | 1.012 | 0.93 |
| 480_V | 484_S | 1.011 | 0.93 |
| 413_P | 478_D | 1.009 | 0.93 |
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 | |
| 4ry2A | 2 | 0 | 100 | 0.356 | Contact Map |
| 4f4cA | 1 | 0.896 | 100 | 0.378 | Contact Map |
| 4a82A | 4 | 0.8727 | 100 | 0.379 | Contact Map |
| 4q4hB | 1 | 0.8758 | 100 | 0.406 | Contact Map |
| 4q9hA | 1 | 0.8742 | 100 | 0.413 | Contact Map |
| 3wmgA | 1 | 0.8727 | 100 | 0.415 | Contact Map |
| 3zdqA | 1 | 0.8696 | 100 | 0.419 | Contact Map |
| 3b60A | 4 | 0.8634 | 100 | 0.421 | Contact Map |
| 3b5xA | 2 | 0.8634 | 100 | 0.423 | Contact Map |
| 4q4hA | 1 | 0.8665 | 100 | 0.424 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)