| rb_01 |
| ID: | 1489782805 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 999 (353) | ||
| Sequences: | 5194 (2943.9) | ||
| Seq/Len: | 14.714 | ||
| Nf(neff/√len): | 156.7 |
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: 14.714).
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 |
| 447_A | 535_L | 3.931 | 1.00 |
| 588_K | 593_E | 3.862 | 1.00 |
| 420_E | 486_K | 3.611 | 1.00 |
| 453_G | 487_I | 3.333 | 1.00 |
| 473_L | 488_A | 3.220 | 1.00 |
| 467_L | 534_L | 3.011 | 1.00 |
| 590_N | 593_E | 2.831 | 1.00 |
| 368_A | 377_V | 2.684 | 1.00 |
| 400_H | 406_S | 2.644 | 1.00 |
| 528_V | 597_S | 2.636 | 1.00 |
| 367_R | 374_E | 2.592 | 1.00 |
| 368_A | 375_V | 2.566 | 1.00 |
| 528_V | 586_C | 2.554 | 1.00 |
| 462_I | 493_A | 2.533 | 1.00 |
| 454_L | 467_L | 2.515 | 1.00 |
| 454_L | 597_S | 2.492 | 1.00 |
| 449_H | 485_A | 2.379 | 1.00 |
| 469_P | 510_F | 2.349 | 1.00 |
| 428_D | 470_H | 2.309 | 1.00 |
| 367_R | 421_L | 2.279 | 1.00 |
| 440_R | 443_Q | 2.250 | 1.00 |
| 506_G | 511_R | 2.240 | 1.00 |
| 466_D | 471_N | 2.121 | 1.00 |
| 365_V | 376_A | 2.116 | 1.00 |
| 532_G | 586_C | 2.072 | 1.00 |
| 468_K | 507_T | 2.018 | 1.00 |
| 451_A | 531_F | 1.994 | 1.00 |
| 472_V | 485_A | 1.978 | 1.00 |
| 469_P | 534_L | 1.928 | 1.00 |
| 597_S | 600_V | 1.828 | 1.00 |
| 407_L | 417_L | 1.813 | 1.00 |
| 455_R | 459_S | 1.805 | 1.00 |
| 454_L | 531_F | 1.775 | 1.00 |
| 450_V | 467_L | 1.770 | 1.00 |
| 406_S | 420_E | 1.746 | 1.00 |
| 532_G | 587_L | 1.743 | 1.00 |
| 450_V | 472_V | 1.732 | 1.00 |
| 428_D | 537_D | 1.727 | 1.00 |
| 542_G | 545_I | 1.668 | 1.00 |
| 401_H | 456_Y | 1.657 | 1.00 |
| 357_R | 360_L | 1.640 | 1.00 |
| 454_L | 487_I | 1.630 | 1.00 |
| 454_L | 458_H | 1.623 | 1.00 |
| 586_C | 600_V | 1.622 | 1.00 |
| 426_S | 429_R | 1.608 | 1.00 |
| 510_F | 537_D | 1.603 | 1.00 |
| 585_Q | 595_P | 1.595 | 1.00 |
| 471_N | 489_D | 1.589 | 1.00 |
| 585_Q | 603_I | 1.587 | 1.00 |
| 377_V | 418_V | 1.585 | 1.00 |
| 522_Y | 526_A | 1.570 | 1.00 |
| 450_V | 534_L | 1.534 | 1.00 |
| 425_G | 433_Q | 1.527 | 1.00 |
| 446_I | 485_A | 1.516 | 1.00 |
| 586_C | 595_P | 1.515 | 1.00 |
| 404_L | 457_L | 1.512 | 1.00 |
| 375_V | 418_V | 1.504 | 1.00 |
| 408_L | 420_E | 1.492 | 1.00 |
| 399_L | 456_Y | 1.475 | 1.00 |
| 449_H | 484_I | 1.474 | 1.00 |
| 512_A | 526_A | 1.458 | 1.00 |
| 366_Y | 379_I | 1.449 | 1.00 |
| 423_S | 481_A | 1.447 | 1.00 |
| 492_I | 505_E | 1.438 | 1.00 |
| 428_D | 432_Q | 1.437 | 1.00 |
| 405_I | 422_A | 1.427 | 1.00 |
| 368_A | 418_V | 1.427 | 1.00 |
| 467_L | 487_I | 1.421 | 1.00 |
| 450_V | 485_A | 1.412 | 1.00 |
| 465_R | 522_Y | 1.386 | 0.99 |
| 582_L | 600_V | 1.385 | 0.99 |
| 455_R | 601_F | 1.368 | 0.99 |
| 472_V | 534_L | 1.361 | 0.99 |
| 512_A | 515_V | 1.347 | 0.99 |
| 595_P | 600_V | 1.344 | 0.99 |
| 466_D | 506_G | 1.340 | 0.99 |
| 468_K | 471_N | 1.320 | 0.99 |
| 426_S | 470_H | 1.312 | 0.99 |
| 515_V | 526_A | 1.299 | 0.99 |
| 439_T | 442_L | 1.295 | 0.99 |
| 536_Y | 587_L | 1.294 | 0.99 |
| 448_L | 452_D | 1.293 | 0.99 |
| 591_P | 594_R | 1.291 | 0.99 |
| 582_L | 595_P | 1.290 | 0.99 |
| 424_K | 483_I | 1.281 | 0.99 |
| 447_A | 538_I | 1.278 | 0.99 |
| 450_V | 453_G | 1.277 | 0.99 |
| 583_I | 587_L | 1.273 | 0.99 |
| 455_R | 598_A | 1.264 | 0.99 |
| 457_L | 462_I | 1.234 | 0.98 |
| 458_H | 468_K | 1.233 | 0.98 |
| 531_F | 586_C | 1.223 | 0.98 |
| 469_P | 537_D | 1.207 | 0.98 |
| 438_L | 443_Q | 1.199 | 0.98 |
| 403_S | 449_H | 1.199 | 0.98 |
| 559_E | 562_G | 1.185 | 0.98 |
| 525_Q | 596_T | 1.179 | 0.98 |
| 431_L | 537_D | 1.178 | 0.98 |
| 404_L | 456_Y | 1.163 | 0.97 |
| 466_D | 491_G | 1.162 | 0.97 |
| 531_F | 535_L | 1.160 | 0.97 |
| 515_V | 522_Y | 1.156 | 0.97 |
| 512_A | 516_A | 1.150 | 0.97 |
| 619_P | 622_V | 1.139 | 0.97 |
| 404_L | 453_G | 1.134 | 0.97 |
| 342_M | 347_T | 1.122 | 0.97 |
| 411_G | 418_V | 1.119 | 0.96 |
| 531_F | 597_S | 1.117 | 0.96 |
| 457_L | 490_Y | 1.115 | 0.96 |
| 446_I | 474_L | 1.113 | 0.96 |
| 451_A | 600_V | 1.100 | 0.96 |
| 315_K | 319_H | 1.099 | 0.96 |
| 464_Y | 471_N | 1.099 | 0.96 |
| 447_A | 531_F | 1.082 | 0.96 |
| 445_R | 449_H | 1.079 | 0.95 |
| 407_L | 419_M | 1.074 | 0.95 |
| 468_K | 489_D | 1.068 | 0.95 |
| 360_L | 363_G | 1.065 | 0.95 |
| 351_V | 358_A | 1.050 | 0.94 |
| 465_R | 505_E | 1.048 | 0.94 |
| 431_L | 538_I | 1.040 | 0.94 |
| 480_N | 484_I | 1.039 | 0.94 |
| 373_E | 406_S | 1.034 | 0.94 |
| 440_R | 444_H | 1.031 | 0.94 |
| 514_E | 527_D | 1.030 | 0.94 |
| 369_A | 374_E | 1.028 | 0.94 |
| 446_I | 472_V | 1.023 | 0.93 |
| 351_V | 357_R | 1.020 | 0.93 |
| 451_A | 601_F | 1.017 | 0.93 |
| 529_Y | 533_L | 1.015 | 0.93 |
| 316_M | 322_E | 1.013 | 0.93 |
| 362_F | 365_V | 1.012 | 0.93 |
| 350_P | 358_A | 1.012 | 0.93 |
| 425_G | 429_R | 1.012 | 0.93 |
| 456_Y | 460_A | 1.005 | 0.93 |
| 362_F | 491_G | 1.002 | 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 | |
| 4gt4A | 2 | 0.2573 | 100 | 0.805 | Contact Map |
| 4aojA | 3 | 0.2523 | 100 | 0.806 | Contact Map |
| 3zonA | 1 | 0.2533 | 100 | 0.807 | Contact Map |
| 4aszA | 1 | 0.2693 | 100 | 0.807 | Contact Map |
| 4aseA | 1 | 0.2793 | 100 | 0.807 | Contact Map |
| 4bkjA | 2 | 0.2613 | 100 | 0.81 | Contact Map |
| 4e5wA | 2 | 0.2683 | 100 | 0.81 | Contact Map |
| 4fvqA | 1 | 0.2583 | 100 | 0.811 | Contact Map |
| 5a46A | 2 | 0 | 100 | 0.811 | Contact Map |
| 4fyoA | 1 | 0.2553 | 100 | 0.811 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)