| Student |
| ID: | 1495815679 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 644 (593) | ||
| Sequences: | 4405 (2321.2) | ||
| Seq/Len: | 7.428 | ||
| Nf(neff/√len): | 95.3 |
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: 7.428).
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 |
| 568_M | 572_H | 5.163 | 1.00 |
| 562_Q | 566_D | 4.480 | 1.00 |
| 328_E | 347_A | 3.958 | 1.00 |
| 169_E | 177_F | 3.863 | 1.00 |
| 540_E | 543_R | 3.611 | 1.00 |
| 479_I | 568_M | 3.531 | 1.00 |
| 551_A | 555_R | 3.491 | 1.00 |
| 377_K | 384_E | 3.453 | 1.00 |
| 466_I | 556_N | 3.421 | 1.00 |
| 321_L | 357_S | 3.371 | 1.00 |
| 40_E | 45_Q | 3.367 | 1.00 |
| 335_M | 365_V | 3.348 | 1.00 |
| 338_V | 380_V | 3.298 | 1.00 |
| 328_E | 332_K | 3.297 | 1.00 |
| 512_K | 544_I | 3.251 | 1.00 |
| 365_V | 385_F | 3.235 | 1.00 |
| 477_E | 561_R | 3.140 | 1.00 |
| 421_I | 467_S | 3.038 | 1.00 |
| 409_E | 576_D | 3.021 | 1.00 |
| 377_K | 381_S | 2.977 | 1.00 |
| 331_L | 361_L | 2.966 | 1.00 |
| 238_E | 242_K | 2.953 | 1.00 |
| 478_I | 564_L | 2.927 | 1.00 |
| 335_M | 346_A | 2.892 | 1.00 |
| 424_L | 563_L | 2.878 | 1.00 |
| 466_I | 552_L | 2.840 | 1.00 |
| 567_N | 570_I | 2.833 | 1.00 |
| 479_I | 571_L | 2.797 | 1.00 |
| 581_Y | 588_Q | 2.795 | 1.00 |
| 467_S | 556_N | 2.780 | 1.00 |
| 179_K | 378_R | 2.750 | 1.00 |
| 479_I | 572_H | 2.748 | 1.00 |
| 561_R | 565_T | 2.728 | 1.00 |
| 427_E | 464_S | 2.713 | 1.00 |
| 424_L | 567_N | 2.702 | 1.00 |
| 512_K | 548_E | 2.609 | 1.00 |
| 469_L | 495_V | 2.581 | 1.00 |
| 550_K | 554_E | 2.579 | 1.00 |
| 572_H | 576_D | 2.570 | 1.00 |
| 496_A | 553_I | 2.566 | 1.00 |
| 477_E | 557_Y | 2.478 | 1.00 |
| 491_N | 494_K | 2.437 | 1.00 |
| 467_S | 560_A | 2.410 | 1.00 |
| 381_S | 384_E | 2.407 | 1.00 |
| 416_A | 574_M | 2.379 | 1.00 |
| 474_L | 561_R | 2.378 | 1.00 |
| 487_T | 507_W | 2.371 | 1.00 |
| 422_G | 448_F | 2.338 | 1.00 |
| 512_K | 547_Q | 2.330 | 1.00 |
| 408_K | 579_M | 2.300 | 1.00 |
| 466_I | 500_A | 2.274 | 1.00 |
| 504_V | 552_L | 2.272 | 1.00 |
| 175_S | 179_K | 2.249 | 1.00 |
| 37_F | 41_V | 2.244 | 1.00 |
| 462_L | 499_L | 2.228 | 1.00 |
| 183_K | 362_A | 2.196 | 1.00 |
| 422_G | 468_T | 2.190 | 1.00 |
| 454_A | 461_K | 2.167 | 1.00 |
| 502_N | 507_W | 2.156 | 1.00 |
| 375_G | 387_K | 2.152 | 1.00 |
| 502_N | 506_Q | 2.142 | 1.00 |
| 558_N | 562_Q | 2.138 | 1.00 |
| 115_V | 119_F | 2.125 | 1.00 |
| 510_S | 548_E | 2.105 | 1.00 |
| 463_E | 556_N | 2.090 | 1.00 |
| 448_F | 468_T | 2.084 | 1.00 |
| 375_G | 384_E | 2.071 | 1.00 |
| 491_N | 495_V | 2.040 | 1.00 |
| 411_T | 456_S | 2.039 | 1.00 |
| 425_V | 464_S | 2.033 | 1.00 |
| 342_P | 379_V | 2.008 | 1.00 |
| 459_R | 463_E | 2.007 | 1.00 |
| 478_I | 565_T | 1.982 | 1.00 |
| 214_F | 243_A | 1.977 | 1.00 |
| 423_R | 590_D | 1.974 | 1.00 |
| 460_Q | 482_P | 1.966 | 1.00 |
| 463_E | 555_R | 1.945 | 1.00 |
| 33_D | 36_T | 1.934 | 1.00 |
| 435_T | 583_T | 1.928 | 1.00 |
| 557_Y | 561_R | 1.899 | 1.00 |
| 576_D | 580_K | 1.898 | 1.00 |
| 577_A | 581_Y | 1.894 | 1.00 |
| 372_A | 384_E | 1.879 | 1.00 |
| 164_V | 205_I | 1.857 | 1.00 |
| 329_Q | 332_K | 1.831 | 1.00 |
| 338_V | 365_V | 1.825 | 1.00 |
| 110_L | 114_G | 1.788 | 1.00 |
| 325_R | 328_E | 1.775 | 1.00 |
| 257_G | 307_L | 1.768 | 1.00 |
| 37_F | 49_A | 1.766 | 1.00 |
| 41_V | 46_V | 1.764 | 1.00 |
| 158_D | 326_G | 1.759 | 1.00 |
| 577_A | 584_I | 1.753 | 1.00 |
| 516_L | 553_I | 1.747 | 1.00 |
| 518_Y | 545_I | 1.742 | 1.00 |
| 341_A | 379_V | 1.737 | 1.00 |
| 554_E | 558_N | 1.734 | 1.00 |
| 410_S | 480_Y | 1.709 | 1.00 |
| 341_A | 381_S | 1.703 | 1.00 |
| 467_S | 559_R | 1.656 | 1.00 |
| 76_K | 79_D | 1.656 | 1.00 |
| 335_M | 385_F | 1.646 | 1.00 |
| 420_I | 571_L | 1.643 | 1.00 |
| 585_D | 588_Q | 1.640 | 1.00 |
| 442_A | 445_V | 1.632 | 1.00 |
| 474_L | 557_Y | 1.631 | 1.00 |
| 406_A | 409_E | 1.630 | 1.00 |
| 176_R | 376_N | 1.619 | 1.00 |
| 203_K | 287_G | 1.618 | 1.00 |
| 570_I | 573_A | 1.609 | 1.00 |
| 434_V | 446_T | 1.607 | 1.00 |
| 410_S | 486_S | 1.597 | 1.00 |
| 241_K | 288_N | 1.588 | 1.00 |
| 420_I | 574_M | 1.586 | 1.00 |
| 405_E | 409_E | 1.578 | 1.00 |
| 464_S | 559_R | 1.576 | 1.00 |
| 558_N | 561_R | 1.567 | 1.00 |
| 58_V | 66_Y | 1.561 | 1.00 |
| 570_I | 593_M | 1.557 | 1.00 |
| 428_H | 464_S | 1.551 | 1.00 |
| 409_E | 480_Y | 1.547 | 1.00 |
| 469_L | 499_L | 1.531 | 1.00 |
| 443_L | 456_S | 1.499 | 0.99 |
| 462_L | 487_T | 1.493 | 0.99 |
| 540_E | 544_I | 1.486 | 0.99 |
| 48_E | 87_K | 1.482 | 0.99 |
| 48_E | 59_T | 1.471 | 0.99 |
| 498_N | 502_N | 1.470 | 0.99 |
| 390_D | 433_K | 1.464 | 0.99 |
| 201_L | 319_V | 1.448 | 0.99 |
| 340_L | 346_A | 1.447 | 0.99 |
| 413_Y | 572_H | 1.445 | 0.99 |
| 428_H | 468_T | 1.429 | 0.99 |
| 431_V | 446_T | 1.422 | 0.99 |
| 559_R | 562_Q | 1.419 | 0.99 |
| 573_A | 595_R | 1.413 | 0.99 |
| 131_A | 134_F | 1.404 | 0.99 |
| 465_Q | 495_V | 1.398 | 0.99 |
| 513_L | 518_Y | 1.385 | 0.99 |
| 413_Y | 576_D | 1.373 | 0.99 |
| 371_F | 384_E | 1.371 | 0.99 |
| 421_I | 471_G | 1.366 | 0.99 |
| 246_C | 291_I | 1.357 | 0.99 |
| 114_G | 118_F | 1.356 | 0.99 |
| 473_R | 489_A | 1.355 | 0.99 |
| 383_V | 387_K | 1.355 | 0.99 |
| 571_L | 575_K | 1.352 | 0.99 |
| 113_I | 117_I | 1.347 | 0.98 |
| 356_F | 364_L | 1.347 | 0.98 |
| 537_M | 542_A | 1.343 | 0.98 |
| 44_D | 84_K | 1.342 | 0.98 |
| 42_N | 80_N | 1.339 | 0.98 |
| 459_R | 511_E | 1.337 | 0.98 |
| 167_L | 188_V | 1.337 | 0.98 |
| 32_V | 58_V | 1.334 | 0.98 |
| 493_I | 517_L | 1.326 | 0.98 |
| 586_A | 590_D | 1.323 | 0.98 |
| 109_M | 113_I | 1.323 | 0.98 |
| 36_T | 39_Q | 1.313 | 0.98 |
| 478_I | 561_R | 1.311 | 0.98 |
| 535_K | 539_D | 1.311 | 0.98 |
| 548_E | 551_A | 1.303 | 0.98 |
| 543_R | 547_Q | 1.303 | 0.98 |
| 577_A | 580_K | 1.300 | 0.98 |
| 36_T | 40_E | 1.294 | 0.98 |
| 458_S | 486_S | 1.294 | 0.98 |
| 421_I | 560_A | 1.289 | 0.98 |
| 480_Y | 486_S | 1.278 | 0.98 |
| 205_I | 294_I | 1.274 | 0.98 |
| 158_D | 329_Q | 1.270 | 0.98 |
| 432_H | 449_L | 1.268 | 0.98 |
| 352_G | 389_K | 1.266 | 0.97 |
| 47_R | 61_K | 1.265 | 0.97 |
| 428_H | 448_F | 1.263 | 0.97 |
| 463_E | 559_R | 1.260 | 0.97 |
| 160_A | 320_G | 1.258 | 0.97 |
| 345_D | 348_I | 1.253 | 0.97 |
| 478_I | 568_M | 1.251 | 0.97 |
| 469_L | 491_N | 1.247 | 0.97 |
| 220_D | 277_Q | 1.243 | 0.97 |
| 504_V | 549_V | 1.243 | 0.97 |
| 565_T | 568_M | 1.241 | 0.97 |
| 457_A | 461_K | 1.217 | 0.97 |
| 434_V | 589_I | 1.217 | 0.97 |
| 577_A | 591_D | 1.206 | 0.96 |
| 157_C | 160_A | 1.204 | 0.96 |
| 39_Q | 43_N | 1.198 | 0.96 |
| 544_I | 547_Q | 1.195 | 0.96 |
| 525_V | 530_S | 1.189 | 0.96 |
| 323_D | 326_G | 1.189 | 0.96 |
| 469_L | 496_A | 1.184 | 0.96 |
| 32_V | 40_E | 1.183 | 0.96 |
| 264_L | 527_L | 1.183 | 0.96 |
| 137_S | 235_D | 1.179 | 0.96 |
| 335_M | 340_L | 1.177 | 0.96 |
| 406_A | 452_G | 1.173 | 0.96 |
| 407_Q | 456_S | 1.168 | 0.95 |
| 574_M | 584_I | 1.167 | 0.95 |
| 424_L | 570_I | 1.167 | 0.95 |
| 240_A | 248_I | 1.165 | 0.95 |
| 262_A | 525_V | 1.165 | 0.95 |
| 259_Q | 529_R | 1.164 | 0.95 |
| 500_A | 504_V | 1.159 | 0.95 |
| 574_M | 592_L | 1.146 | 0.95 |
| 410_S | 456_S | 1.137 | 0.94 |
| 474_L | 560_A | 1.134 | 0.94 |
| 474_L | 565_T | 1.133 | 0.94 |
| 564_L | 571_L | 1.129 | 0.94 |
| 573_A | 577_A | 1.127 | 0.94 |
| 460_Q | 464_S | 1.120 | 0.94 |
| 79_D | 83_T | 1.119 | 0.94 |
| 162_E | 165_A | 1.119 | 0.94 |
| 246_C | 290_G | 1.118 | 0.94 |
| 587_P | 591_D | 1.116 | 0.94 |
| 165_A | 169_E | 1.114 | 0.94 |
| 409_E | 413_Y | 1.113 | 0.94 |
| 574_M | 589_I | 1.113 | 0.94 |
| 513_L | 545_I | 1.110 | 0.93 |
| 463_E | 467_S | 1.107 | 0.93 |
| 573_A | 592_L | 1.104 | 0.93 |
| 112_L | 115_V | 1.102 | 0.93 |
| 193_P | 320_G | 1.101 | 0.93 |
| 412_A | 579_M | 1.098 | 0.93 |
| 588_Q | 591_D | 1.095 | 0.93 |
| 258_R | 302_V | 1.090 | 0.93 |
| 560_A | 563_L | 1.090 | 0.93 |
| 394_M | 401_M | 1.088 | 0.93 |
| 466_I | 496_A | 1.080 | 0.92 |
| 163_E | 396_A | 1.079 | 0.92 |
| 116_W | 120_M | 1.078 | 0.92 |
| 403_M | 443_L | 1.078 | 0.92 |
| 239_Q | 242_K | 1.068 | 0.92 |
| 169_E | 173_E | 1.068 | 0.92 |
| 421_I | 563_L | 1.067 | 0.92 |
| 416_A | 575_K | 1.066 | 0.92 |
| 386_E | 432_H | 1.066 | 0.92 |
| 590_D | 594_A | 1.065 | 0.92 |
| 390_D | 445_V | 1.062 | 0.91 |
| 262_A | 526_F | 1.062 | 0.91 |
| 512_K | 551_A | 1.061 | 0.91 |
| 37_F | 58_V | 1.059 | 0.91 |
| 157_C | 326_G | 1.055 | 0.91 |
| 526_F | 529_R | 1.053 | 0.91 |
| 525_V | 528_G | 1.053 | 0.91 |
| 50_R | 91_E | 1.047 | 0.91 |
| 425_V | 428_H | 1.047 | 0.91 |
| 32_V | 37_F | 1.046 | 0.91 |
| 423_R | 589_I | 1.046 | 0.91 |
| 505_T | 545_I | 1.045 | 0.90 |
| 525_V | 529_R | 1.042 | 0.90 |
| 180_L | 373_A | 1.042 | 0.90 |
| 349_I | 385_F | 1.039 | 0.90 |
| 461_K | 465_Q | 1.034 | 0.90 |
| 68_T | 71_P | 1.033 | 0.90 |
| 325_R | 329_Q | 1.031 | 0.90 |
| 495_V | 498_N | 1.031 | 0.90 |
| 352_G | 391_K | 1.031 | 0.90 |
| 347_A | 351_R | 1.029 | 0.90 |
| 66_Y | 69_Y | 1.028 | 0.90 |
| 184_I | 292_I | 1.026 | 0.89 |
| 111_L | 114_G | 1.023 | 0.89 |
| 391_K | 394_M | 1.022 | 0.89 |
| 429_D | 465_Q | 1.020 | 0.89 |
| 416_A | 420_I | 1.018 | 0.89 |
| 448_F | 469_L | 1.017 | 0.89 |
| 253_I | 256_V | 1.014 | 0.89 |
| 331_L | 349_I | 1.010 | 0.88 |
| 149_T | 203_K | 1.006 | 0.88 |
| 456_S | 486_S | 1.006 | 0.88 |
| 552_L | 556_N | 1.005 | 0.88 |
| 166_E | 374_R | 1.004 | 0.88 |
| 413_Y | 575_K | 1.004 | 0.88 |
| 510_S | 551_A | 1.004 | 0.88 |
| 470_Y | 496_A | 1.004 | 0.88 |
| 462_L | 507_W | 1.003 | 0.88 |
| 556_N | 559_R | 1.002 | 0.88 |
| 465_Q | 469_L | 1.001 | 0.88 |
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 | |
| 2ce7A | 6 | 0.6693 | 100 | 0.464 | Contact Map |
| 4ww0A | 3 | 0 | 100 | 0.468 | Contact Map |
| 2dhrA | 6 | 0.7112 | 100 | 0.491 | Contact Map |
| 4cr2J | 1 | 0.5497 | 100 | 0.727 | Contact Map |
| 4cr2I | 1 | 0.545 | 100 | 0.733 | Contact Map |
| 2di4A | 2 | 0.2717 | 100 | 0.735 | Contact Map |
| 4cr2K | 1 | 0.5683 | 100 | 0.748 | Contact Map |
| 4cr2L | 1 | 0.5 | 100 | 0.754 | Contact Map |
| 4cr2M | 1 | 0.5295 | 100 | 0.758 | Contact Map |
| 2x8aA | 1 | 0.3587 | 100 | 0.758 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)