| ccka |
| ID: | 1433157620 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 691 (632) | ||
| Sequences: | 3970 (3494.3) | ||
| Seq/Len: | 6.282 | ||
| Nf(neff/√len): | 139.0 |
Jackhmmer Results: (2015_01_07)
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: 6.282).
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 |
| 598_L | 617_I | 5.342 | 1.00 |
| 335_L | 355_I | 4.173 | 1.00 |
| 378_V | 382_V | 3.928 | 1.00 |
| 622_S | 634_L | 3.552 | 1.00 |
| 383_L | 419_A | 3.506 | 1.00 |
| 206_F | 292_I | 3.497 | 1.00 |
| 529_R | 532_E | 3.389 | 1.00 |
| 489_M | 526_V | 3.376 | 1.00 |
| 602_D | 628_G | 3.013 | 1.00 |
| 583_R | 599_E | 3.009 | 1.00 |
| 485_P | 488_V | 2.925 | 1.00 |
| 630_D | 633_T | 2.802 | 1.00 |
| 572_R | 596_E | 2.770 | 1.00 |
| 601_A | 605_E | 2.719 | 1.00 |
| 432_A | 450_I | 2.695 | 1.00 |
| 525_H | 537_R | 2.657 | 1.00 |
| 298_K | 301_E | 2.635 | 1.00 |
| 637_K | 640_G | 2.615 | 1.00 |
| 600_A | 609_I | 2.610 | 1.00 |
| 576_V | 606_A | 2.595 | 1.00 |
| 604_E | 628_G | 2.547 | 1.00 |
| 332_Q | 359_G | 2.532 | 1.00 |
| 577_E | 583_R | 2.445 | 1.00 |
| 209_A | 289_A | 2.444 | 1.00 |
| 611_E | 641_Y | 2.441 | 1.00 |
| 194_P | 198_D | 2.416 | 1.00 |
| 484_I | 488_V | 2.381 | 1.00 |
| 514_Y | 518_K | 2.354 | 1.00 |
| 622_S | 635_L | 2.235 | 1.00 |
| 607_L | 634_L | 2.217 | 1.00 |
| 610_A | 638_A | 2.207 | 1.00 |
| 344_V | 348_S | 2.199 | 1.00 |
| 485_P | 530_P | 2.195 | 1.00 |
| 635_L | 647_V | 2.180 | 1.00 |
| 379_Q | 382_V | 2.135 | 1.00 |
| 419_A | 520_S | 2.121 | 1.00 |
| 474_F | 537_R | 2.120 | 1.00 |
| 478_S | 535_A | 2.102 | 1.00 |
| 572_R | 598_L | 2.088 | 1.00 |
| 577_E | 626_M | 2.086 | 1.00 |
| 427_A | 516_I | 2.056 | 1.00 |
| 475_I | 538_I | 2.037 | 1.00 |
| 442_A | 480_D | 2.014 | 1.00 |
| 474_F | 539_F | 2.003 | 1.00 |
| 265_E | 298_K | 1.997 | 1.00 |
| 427_A | 517_V | 1.993 | 1.00 |
| 301_E | 305_S | 1.993 | 1.00 |
| 513_V | 524_I | 1.987 | 1.00 |
| 409_D | 451_R | 1.982 | 1.00 |
| 575_F | 586_A | 1.974 | 1.00 |
| 526_V | 536_F | 1.974 | 1.00 |
| 648_M | 683_R | 1.969 | 1.00 |
| 619_L | 684_V | 1.944 | 1.00 |
| 297_Q | 301_E | 1.941 | 1.00 |
| 593_R | 681_A | 1.941 | 1.00 |
| 518_K | 523_W | 1.916 | 1.00 |
| 603_G | 634_L | 1.914 | 1.00 |
| 245_D | 248_S | 1.910 | 1.00 |
| 207_G | 231_M | 1.902 | 1.00 |
| 517_V | 538_I | 1.885 | 1.00 |
| 234_A | 271_D | 1.885 | 1.00 |
| 649_F | 667_G | 1.870 | 1.00 |
| 602_D | 605_E | 1.866 | 1.00 |
| 583_R | 601_A | 1.841 | 1.00 |
| 212_E | 218_T | 1.840 | 1.00 |
| 604_E | 608_I | 1.825 | 1.00 |
| 579_E | 582_V | 1.790 | 1.00 |
| 575_F | 597_V | 1.781 | 1.00 |
| 660_D | 664_G | 1.754 | 1.00 |
| 613_N | 617_I | 1.740 | 1.00 |
| 248_S | 267_R | 1.724 | 1.00 |
| 635_L | 667_G | 1.722 | 1.00 |
| 629_I | 637_K | 1.716 | 1.00 |
| 476_E | 535_A | 1.715 | 1.00 |
| 493_F | 524_I | 1.715 | 1.00 |
| 451_R | 478_S | 1.708 | 1.00 |
| 639_R | 668_V | 1.702 | 1.00 |
| 620_L | 645_A | 1.699 | 1.00 |
| 453_A | 476_E | 1.698 | 1.00 |
| 311_Q | 315_Q | 1.691 | 1.00 |
| 488_V | 491_K | 1.690 | 1.00 |
| 573_I | 595_Y | 1.682 | 1.00 |
| 451_R | 476_E | 1.678 | 1.00 |
| 330_A | 358_T | 1.668 | 1.00 |
| 449_R | 478_S | 1.664 | 1.00 |
| 669_T | 683_R | 1.664 | 1.00 |
| 209_A | 221_V | 1.659 | 1.00 |
| 304_L | 308_Q | 1.657 | 1.00 |
| 476_E | 537_R | 1.652 | 1.00 |
| 212_E | 220_R | 1.637 | 1.00 |
| 207_G | 291_M | 1.628 | 1.00 |
| 396_L | 432_A | 1.622 | 1.00 |
| 384_D | 387_E | 1.611 | 1.00 |
| 183_P | 187_A | 1.599 | 1.00 |
| 669_T | 687_Q | 1.589 | 0.99 |
| 587_A | 599_E | 1.585 | 0.99 |
| 587_A | 591_R | 1.574 | 0.99 |
| 428_V | 475_I | 1.574 | 0.99 |
| 342_H | 348_S | 1.572 | 0.99 |
| 334_R | 585_V | 1.572 | 0.99 |
| 453_A | 474_F | 1.572 | 0.99 |
| 204_S | 208_A | 1.551 | 0.99 |
| 527_H | 535_A | 1.550 | 0.99 |
| 374_R | 506_T | 1.548 | 0.99 |
| 452_T | 475_I | 1.528 | 0.99 |
| 339_L | 349_Y | 1.525 | 0.99 |
| 573_I | 619_L | 1.522 | 0.99 |
| 576_V | 600_A | 1.521 | 0.99 |
| 427_A | 513_V | 1.520 | 0.99 |
| 603_G | 629_I | 1.516 | 0.99 |
| 576_V | 634_L | 1.515 | 0.99 |
| 94_A | 102_V | 1.508 | 0.99 |
| 270_R | 274_R | 1.500 | 0.99 |
| 409_D | 449_R | 1.492 | 0.99 |
| 190_A | 193_P | 1.488 | 0.99 |
| 624_V | 649_F | 1.487 | 0.99 |
| 396_L | 439_V | 1.484 | 0.99 |
| 610_A | 620_L | 1.484 | 0.99 |
| 598_L | 609_I | 1.482 | 0.99 |
| 484_I | 489_M | 1.469 | 0.99 |
| 442_A | 446_G | 1.467 | 0.99 |
| 201_A | 223_E | 1.458 | 0.99 |
| 227_A | 230_T | 1.454 | 0.99 |
| 339_L | 353_N | 1.454 | 0.99 |
| 571_G | 595_Y | 1.440 | 0.99 |
| 633_T | 637_K | 1.433 | 0.99 |
| 651_S | 670_F | 1.425 | 0.99 |
| 115_E | 159_L | 1.422 | 0.99 |
| 347_P | 588_R | 1.421 | 0.99 |
| 572_R | 617_I | 1.419 | 0.99 |
| 345_G | 348_S | 1.412 | 0.99 |
| 472_T | 541_P | 1.408 | 0.98 |
| 578_D | 626_M | 1.406 | 0.98 |
| 486_P | 529_R | 1.395 | 0.98 |
| 484_I | 492_I | 1.394 | 0.98 |
| 179_E | 182_S | 1.386 | 0.98 |
| 669_T | 686_Q | 1.384 | 0.98 |
| 427_A | 538_I | 1.383 | 0.98 |
| 574_L | 600_A | 1.376 | 0.98 |
| 447_V | 480_D | 1.374 | 0.98 |
| 384_D | 416_Q | 1.372 | 0.98 |
| 368_K | 423_Q | 1.365 | 0.98 |
| 625_I | 653_Y | 1.360 | 0.98 |
| 193_P | 196_S | 1.358 | 0.98 |
| 629_I | 633_T | 1.358 | 0.98 |
| 209_A | 228_L | 1.357 | 0.98 |
| 300_I | 304_L | 1.350 | 0.98 |
| 620_L | 638_A | 1.348 | 0.98 |
| 184_A | 187_A | 1.344 | 0.98 |
| 522_G | 541_P | 1.344 | 0.98 |
| 210_L | 286_R | 1.338 | 0.98 |
| 83_E | 87_E | 1.338 | 0.98 |
| 598_L | 613_N | 1.337 | 0.98 |
| 235_K | 238_V | 1.327 | 0.98 |
| 405_K | 447_V | 1.322 | 0.97 |
| 389_I | 452_T | 1.321 | 0.97 |
| 607_L | 610_A | 1.316 | 0.97 |
| 197_L | 200_F | 1.311 | 0.97 |
| 610_A | 645_A | 1.306 | 0.97 |
| 578_D | 631_G | 1.302 | 0.97 |
| 351_G | 588_R | 1.298 | 0.97 |
| 683_R | 686_Q | 1.297 | 0.97 |
| 381_E | 421_K | 1.295 | 0.97 |
| 423_Q | 426_T | 1.295 | 0.97 |
| 170_P | 173_V | 1.290 | 0.97 |
| 338_L | 348_S | 1.290 | 0.97 |
| 508_L | 512_T | 1.290 | 0.97 |
| 382_V | 418_R | 1.288 | 0.97 |
| 224_T | 228_L | 1.288 | 0.97 |
| 568_S | 595_Y | 1.282 | 0.97 |
| 439_V | 448_V | 1.279 | 0.97 |
| 350_E | 584_S | 1.270 | 0.97 |
| 187_A | 191_A | 1.262 | 0.96 |
| 336_D | 356_R | 1.262 | 0.96 |
| 330_A | 581_A | 1.261 | 0.96 |
| 621_I | 680_L | 1.258 | 0.96 |
| 299_Q | 303_Q | 1.258 | 0.96 |
| 607_L | 629_I | 1.257 | 0.96 |
| 472_T | 539_F | 1.255 | 0.96 |
| 407_I | 447_V | 1.254 | 0.96 |
| 330_A | 334_R | 1.253 | 0.96 |
| 380_R | 419_A | 1.250 | 0.96 |
| 391_E | 425_E | 1.250 | 0.96 |
| 415_P | 454_R | 1.249 | 0.96 |
| 92_P | 112_V | 1.248 | 0.96 |
| 338_L | 352_L | 1.245 | 0.96 |
| 400_L | 448_V | 1.239 | 0.96 |
| 374_R | 498_T | 1.239 | 0.96 |
| 580_D | 583_R | 1.235 | 0.96 |
| 324_F | 328_L | 1.234 | 0.96 |
| 624_V | 632_P | 1.233 | 0.96 |
| 302_L | 305_S | 1.218 | 0.95 |
| 489_M | 528_S | 1.217 | 0.95 |
| 486_P | 489_M | 1.216 | 0.95 |
| 386_G | 452_T | 1.215 | 0.95 |
| 426_T | 516_I | 1.208 | 0.95 |
| 407_I | 449_R | 1.207 | 0.95 |
| 188_E | 191_A | 1.205 | 0.95 |
| 335_L | 352_L | 1.199 | 0.95 |
| 198_D | 202_G | 1.198 | 0.95 |
| 626_M | 629_I | 1.196 | 0.95 |
| 191_A | 194_P | 1.191 | 0.95 |
| 492_I | 526_V | 1.190 | 0.94 |
| 329_T | 582_V | 1.188 | 0.94 |
| 606_A | 634_L | 1.187 | 0.94 |
| 441_A | 498_T | 1.185 | 0.94 |
| 337_E | 351_G | 1.184 | 0.94 |
| 130_A | 133_V | 1.182 | 0.94 |
| 679_T | 682_E | 1.181 | 0.94 |
| 498_T | 504_E | 1.181 | 0.94 |
| 393_E | 408_T | 1.181 | 0.94 |
| 392_F | 432_A | 1.180 | 0.94 |
| 211_L | 221_V | 1.178 | 0.94 |
| 603_G | 627_P | 1.173 | 0.94 |
| 97_A | 101_R | 1.172 | 0.94 |
| 609_I | 617_I | 1.172 | 0.94 |
| 234_A | 238_V | 1.169 | 0.94 |
| 354_E | 358_T | 1.167 | 0.94 |
| 650_I | 675_I | 1.159 | 0.93 |
| 608_I | 612_E | 1.159 | 0.93 |
| 676_D | 679_T | 1.156 | 0.93 |
| 647_V | 667_G | 1.149 | 0.93 |
| 307_A | 310_M | 1.144 | 0.93 |
| 107_G | 111_E | 1.143 | 0.93 |
| 578_D | 627_P | 1.143 | 0.93 |
| 335_L | 356_R | 1.142 | 0.93 |
| 600_A | 606_A | 1.139 | 0.93 |
| 578_D | 623_D | 1.135 | 0.92 |
| 341_R | 592_A | 1.134 | 0.92 |
| 589_L | 677_I | 1.134 | 0.92 |
| 517_V | 522_G | 1.133 | 0.92 |
| 339_L | 356_R | 1.129 | 0.92 |
| 225_N | 228_L | 1.128 | 0.92 |
| 303_Q | 306_Q | 1.126 | 0.92 |
| 328_L | 366_V | 1.126 | 0.92 |
| 333_L | 337_E | 1.125 | 0.92 |
| 314_G | 376_Q | 1.125 | 0.92 |
| 501_P | 504_E | 1.122 | 0.92 |
| 423_Q | 516_I | 1.120 | 0.92 |
| 494_D | 497_F | 1.120 | 0.92 |
| 108_P | 111_E | 1.119 | 0.92 |
| 184_A | 188_E | 1.118 | 0.92 |
| 608_I | 611_E | 1.112 | 0.91 |
| 600_A | 603_G | 1.109 | 0.91 |
| 210_L | 225_N | 1.104 | 0.91 |
| 320_V | 369_L | 1.102 | 0.91 |
| 296_E | 299_Q | 1.100 | 0.91 |
| 450_I | 475_I | 1.098 | 0.91 |
| 417_V | 542_V | 1.096 | 0.91 |
| 335_L | 359_G | 1.094 | 0.91 |
| 333_L | 585_V | 1.094 | 0.91 |
| 513_V | 538_I | 1.091 | 0.90 |
| 495_P | 515_G | 1.090 | 0.90 |
| 254_T | 258_E | 1.079 | 0.90 |
| 371_A | 423_Q | 1.079 | 0.90 |
| 207_G | 228_L | 1.079 | 0.90 |
| 389_I | 408_T | 1.074 | 0.89 |
| 570_A | 595_Y | 1.072 | 0.89 |
| 123_V | 127_S | 1.072 | 0.89 |
| 639_R | 645_A | 1.072 | 0.89 |
| 194_P | 197_L | 1.071 | 0.89 |
| 297_Q | 300_I | 1.070 | 0.89 |
| 273_S | 277_H | 1.068 | 0.89 |
| 338_L | 355_I | 1.063 | 0.89 |
| 603_G | 626_M | 1.062 | 0.89 |
| 500_K | 503_G | 1.060 | 0.89 |
| 419_A | 542_V | 1.057 | 0.88 |
| 447_V | 478_S | 1.056 | 0.88 |
| 180_D | 184_A | 1.056 | 0.88 |
| 528_S | 532_E | 1.055 | 0.88 |
| 683_R | 687_Q | 1.055 | 0.88 |
| 634_L | 638_A | 1.054 | 0.88 |
| 657_E | 660_D | 1.052 | 0.88 |
| 526_V | 534_A | 1.051 | 0.88 |
| 389_I | 475_I | 1.049 | 0.88 |
| 180_D | 183_P | 1.048 | 0.88 |
| 622_S | 649_F | 1.048 | 0.88 |
| 331_I | 359_G | 1.047 | 0.88 |
| 229_T | 235_K | 1.044 | 0.88 |
| 620_L | 647_V | 1.043 | 0.88 |
| 185_P | 188_E | 1.042 | 0.87 |
| 267_R | 277_H | 1.036 | 0.87 |
| 219_S | 225_N | 1.035 | 0.87 |
| 396_L | 429_M | 1.033 | 0.87 |
| 356_R | 360_V | 1.032 | 0.87 |
| 662_L | 667_G | 1.032 | 0.87 |
| 620_L | 634_L | 1.031 | 0.87 |
| 115_E | 119_L | 1.031 | 0.87 |
| 323_D | 498_T | 1.030 | 0.87 |
| 624_V | 667_G | 1.028 | 0.87 |
| 622_S | 647_V | 1.028 | 0.87 |
| 624_V | 662_L | 1.025 | 0.86 |
| 324_F | 365_L | 1.024 | 0.86 |
| 276_A | 279_Y | 1.022 | 0.86 |
| 245_D | 267_R | 1.020 | 0.86 |
| 330_A | 365_L | 1.019 | 0.86 |
| 482_P | 503_G | 1.018 | 0.86 |
| 626_M | 634_L | 1.015 | 0.86 |
| 179_E | 183_P | 1.014 | 0.86 |
| 226_P | 230_T | 1.014 | 0.86 |
| 269_A | 275_I | 1.013 | 0.85 |
| 229_T | 236_A | 1.011 | 0.85 |
| 326_N | 362_A | 1.011 | 0.85 |
| 492_I | 536_F | 1.005 | 0.85 |
| 538_I | 541_P | 1.004 | 0.85 |
| 449_R | 480_D | 1.003 | 0.85 |
| 331_I | 355_I | 1.002 | 0.85 |
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 | |
| 3a0rA | 1 | 0.4631 | 100 | 0.54 | Contact Map |
| 4gczA | 2 | 0.5094 | 100 | 0.609 | Contact Map |
| 4i5sA | 2 | 0.5441 | 100 | 0.636 | Contact Map |
| 4r3aA | 2 | 0.4356 | 100 | 0.667 | Contact Map |
| 4mpcA | 1 | 0.4689 | 100 | 0.712 | Contact Map |
| 3jz3A | 2 | 0.2272 | 100 | 0.715 | Contact Map |
| 4e01A | 1 | 0.4038 | 100 | 0.715 | Contact Map |
| 3d36A | 2 | 0.3184 | 100 | 0.716 | Contact Map |
| 4q20A | 2 | 0.3198 | 100 | 0.716 | Contact Map |
| 2c2aA | 1 | 0.3314 | 100 | 0.721 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)