| MSA PKC jack |
| ID: | 1497478914 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 672 (341) | ||
| Sequences: | 129289 (71798.6) | ||
| Seq/Len: | 379.147 | ||
| Nf(neff/√len): | 3888.1 |
Jackhmmer Results: (2016_04)
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: 379.147).
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 |
| 574_T | 579_K | 3.660 | 1.00 |
| 444_A | 528_L | 3.541 | 1.00 |
| 470_M | 480_A | 3.482 | 1.00 |
| 355_L | 364_L | 3.332 | 1.00 |
| 343_M | 355_L | 3.250 | 1.00 |
| 521_W | 572_L | 3.050 | 1.00 |
| 437_E | 562_S | 2.983 | 1.00 |
| 356_A | 365_Y | 2.846 | 1.00 |
| 356_A | 367_I | 2.699 | 1.00 |
| 344_V | 352_K | 2.663 | 1.00 |
| 418_E | 478_K | 2.534 | 1.00 |
| 571_G | 581_L | 2.525 | 1.00 |
| 452_F | 456_K | 2.511 | 1.00 |
| 358_R | 361_T | 2.496 | 1.00 |
| 446_E | 477_I | 2.488 | 1.00 |
| 395_D | 402_Q | 2.445 | 1.00 |
| 344_V | 347_K | 2.435 | 1.00 |
| 465_K | 501_T | 2.431 | 1.00 |
| 426_M | 467_D | 2.392 | 1.00 |
| 446_E | 476_H | 2.309 | 1.00 |
| 452_F | 589_R | 2.284 | 1.00 |
| 396_K | 399_F | 2.271 | 1.00 |
| 472_D | 476_H | 2.263 | 1.00 |
| 340_N | 357_D | 2.248 | 1.00 |
| 421_N | 473_S | 2.241 | 1.00 |
| 576_H | 579_K | 2.239 | 1.00 |
| 451_L | 524_Y | 2.202 | 1.00 |
| 500_G | 505_I | 2.192 | 1.00 |
| 448_S | 524_Y | 2.185 | 1.00 |
| 340_N | 359_K | 2.146 | 1.00 |
| 469_V | 477_I | 2.126 | 1.00 |
| 464_L | 527_L | 2.100 | 1.00 |
| 404_H | 418_E | 2.086 | 1.00 |
| 355_L | 419_Y | 2.080 | 1.00 |
| 447_I | 469_V | 2.073 | 1.00 |
| 436_K | 439_Q | 2.047 | 1.00 |
| 567_S | 594_H | 2.032 | 1.00 |
| 338_D | 358_R | 2.024 | 1.00 |
| 424_D | 427_Y | 1.903 | 1.00 |
| 342_L | 357_D | 1.891 | 1.00 |
| 357_D | 364_L | 1.869 | 1.00 |
| 451_L | 464_L | 1.856 | 1.00 |
| 525_G | 572_L | 1.851 | 1.00 |
| 506_A | 519_V | 1.827 | 1.00 |
| 402_Q | 418_E | 1.825 | 1.00 |
| 521_W | 583_C | 1.815 | 1.00 |
| 450_G | 479_I | 1.764 | 1.00 |
| 440_A | 532_L | 1.762 | 1.00 |
| 367_I | 416_V | 1.708 | 1.00 |
| 466_L | 504_Y | 1.707 | 1.00 |
| 532_L | 565_A | 1.693 | 1.00 |
| 451_L | 583_C | 1.686 | 1.00 |
| 504_Y | 530_E | 1.668 | 1.00 |
| 444_A | 531_M | 1.660 | 1.00 |
| 344_V | 354_M | 1.656 | 1.00 |
| 452_F | 592_R | 1.641 | 1.00 |
| 442_F | 446_E | 1.640 | 1.00 |
| 396_K | 453_F | 1.621 | 1.00 |
| 443_Y | 477_I | 1.615 | 1.00 |
| 444_A | 524_Y | 1.611 | 1.00 |
| 469_V | 527_L | 1.595 | 1.00 |
| 472_D | 478_K | 1.595 | 1.00 |
| 568_V | 581_L | 1.582 | 1.00 |
| 448_S | 591_V | 1.579 | 1.00 |
| 399_F | 449_I | 1.573 | 1.00 |
| 357_D | 362_E | 1.567 | 1.00 |
| 459_I | 485_C | 1.545 | 1.00 |
| 342_L | 355_L | 1.534 | 1.00 |
| 423_G | 431_Q | 1.526 | 1.00 |
| 363_E | 404_H | 1.497 | 1.00 |
| 462_R | 515_Y | 1.486 | 1.00 |
| 426_M | 430_Q | 1.477 | 1.00 |
| 528_L | 568_V | 1.474 | 1.00 |
| 445_A | 449_I | 1.459 | 1.00 |
| 369_I | 412_R | 1.442 | 1.00 |
| 365_Y | 416_V | 1.434 | 1.00 |
| 581_L | 591_V | 1.428 | 1.00 |
| 399_F | 450_G | 1.423 | 1.00 |
| 572_L | 591_V | 1.419 | 1.00 |
| 347_K | 352_K | 1.414 | 1.00 |
| 426_M | 530_E | 1.411 | 1.00 |
| 518_S | 582_G | 1.407 | 0.99 |
| 458_G | 517_K | 1.400 | 0.99 |
| 420_V | 478_K | 1.397 | 0.99 |
| 453_F | 457_R | 1.387 | 0.99 |
| 353_V | 366_A | 1.378 | 0.99 |
| 566_V | 570_K | 1.370 | 0.99 |
| 567_S | 571_G | 1.363 | 0.99 |
| 582_G | 590_D | 1.362 | 0.99 |
| 506_A | 509_I | 1.357 | 0.99 |
| 463_D | 468_N | 1.353 | 0.99 |
| 569_C | 573_M | 1.352 | 0.99 |
| 568_V | 572_L | 1.345 | 0.99 |
| 401_T | 420_V | 1.339 | 0.99 |
| 364_L | 419_Y | 1.325 | 0.99 |
| 440_A | 531_M | 1.324 | 0.99 |
| 447_I | 477_I | 1.310 | 0.99 |
| 466_L | 527_L | 1.300 | 0.99 |
| 393_L | 457_R | 1.296 | 0.99 |
| 553_H | 575_K | 1.292 | 0.99 |
| 530_E | 536_P | 1.288 | 0.99 |
| 354_M | 369_I | 1.287 | 0.99 |
| 462_R | 499_C | 1.284 | 0.99 |
| 420_V | 470_M | 1.284 | 0.99 |
| 449_I | 592_R | 1.279 | 0.99 |
| 557_Y | 566_V | 1.275 | 0.99 |
| 432_V | 439_Q | 1.265 | 0.99 |
| 429_I | 530_E | 1.249 | 0.99 |
| 401_T | 417_M | 1.248 | 0.99 |
| 401_T | 480_A | 1.245 | 0.98 |
| 456_K | 589_R | 1.242 | 0.98 |
| 509_I | 519_V | 1.224 | 0.98 |
| 522_W | 550_I | 1.222 | 0.98 |
| 369_I | 414_Y | 1.213 | 0.98 |
| 526_V | 536_P | 1.209 | 0.98 |
| 420_V | 472_D | 1.206 | 0.98 |
| 403_L | 406_C | 1.202 | 0.98 |
| 400_L | 454_L | 1.201 | 0.98 |
| 372_K | 408_Q | 1.200 | 0.98 |
| 341_F | 354_M | 1.199 | 0.98 |
| 515_Y | 519_V | 1.197 | 0.98 |
| 571_G | 574_T | 1.191 | 0.98 |
| 548_Q | 552_E | 1.187 | 0.98 |
| 342_L | 364_L | 1.187 | 0.98 |
| 390_V | 485_C | 1.168 | 0.97 |
| 461_Y | 464_L | 1.166 | 0.97 |
| 339_F | 405_S | 1.161 | 0.97 |
| 471_L | 477_I | 1.160 | 0.97 |
| 393_L | 487_E | 1.159 | 0.97 |
| 524_Y | 572_L | 1.158 | 0.97 |
| 448_S | 592_R | 1.157 | 0.97 |
| 468_N | 481_D | 1.156 | 0.97 |
| 420_V | 480_A | 1.154 | 0.97 |
| 428_H | 471_L | 1.153 | 0.97 |
| 423_G | 480_A | 1.153 | 0.97 |
| 572_L | 581_L | 1.149 | 0.97 |
| 403_L | 415_F | 1.144 | 0.97 |
| 365_Y | 404_H | 1.142 | 0.97 |
| 445_A | 592_R | 1.137 | 0.97 |
| 407_F | 414_Y | 1.136 | 0.97 |
| 466_L | 530_E | 1.130 | 0.97 |
| 484_M | 499_C | 1.127 | 0.97 |
| 364_L | 421_N | 1.119 | 0.96 |
| 407_F | 416_V | 1.113 | 0.96 |
| 367_I | 414_Y | 1.113 | 0.96 |
| 559_K | 566_V | 1.112 | 0.96 |
| 583_C | 591_V | 1.111 | 0.96 |
| 442_F | 476_H | 1.111 | 0.96 |
| 428_H | 435_F | 1.110 | 0.96 |
| 574_T | 581_L | 1.108 | 0.96 |
| 437_E | 596_F | 1.105 | 0.96 |
| 358_R | 363_E | 1.105 | 0.96 |
| 435_F | 443_Y | 1.102 | 0.96 |
| 449_I | 452_F | 1.102 | 0.96 |
| 571_G | 590_D | 1.100 | 0.96 |
| 448_S | 583_C | 1.090 | 0.96 |
| 381_V | 385_M | 1.089 | 0.96 |
| 394_L | 453_F | 1.088 | 0.96 |
| 447_I | 464_L | 1.087 | 0.96 |
| 424_D | 467_D | 1.085 | 0.96 |
| 464_L | 479_I | 1.083 | 0.96 |
| 526_V | 573_M | 1.077 | 0.95 |
| 391_L | 403_L | 1.076 | 0.95 |
| 399_F | 476_H | 1.073 | 0.95 |
| 394_L | 459_I | 1.070 | 0.95 |
| 549_S | 553_H | 1.066 | 0.95 |
| 345_L | 419_Y | 1.058 | 0.95 |
| 452_F | 583_C | 1.055 | 0.95 |
| 335_K | 338_D | 1.047 | 0.94 |
| 428_H | 432_V | 1.045 | 0.94 |
| 568_V | 591_V | 1.045 | 0.94 |
| 447_I | 527_L | 1.039 | 0.94 |
| 588_E | 591_V | 1.036 | 0.94 |
| 391_L | 417_M | 1.036 | 0.94 |
| 542_D | 545_E | 1.029 | 0.94 |
| 455_H | 583_C | 1.021 | 0.93 |
| 454_L | 459_I | 1.017 | 0.93 |
| 454_L | 482_F | 1.017 | 0.93 |
| 366_A | 419_Y | 1.009 | 0.93 |
| 385_M | 389_R | 1.009 | 0.93 |
| 422_G | 475_G | 1.008 | 0.93 |
| 509_I | 515_Y | 1.001 | 0.92 |
| 341_F | 356_A | 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 | |
| 3pfqA | 1 | 0.7738 | 100 | 0.236 | Contact Map |
| 2i0eA | 2 | 0.4851 | 100 | 0.405 | Contact Map |
| 4gv1A | 1 | 0.4807 | 100 | 0.423 | Contact Map |
| 3txoA | 1 | 0.4688 | 100 | 0.426 | Contact Map |
| 4dc2A | 1 | 0.4807 | 100 | 0.427 | Contact Map |
| 4lqsA | 1 | 0.506 | 100 | 0.436 | Contact Map |
| 1xjdA | 1 | 0.4137 | 100 | 0.436 | Contact Map |
| 4fr4A | 6 | 0.4807 | 100 | 0.438 | Contact Map |
| 3a8xA | 2 | 0.4926 | 100 | 0.442 | Contact Map |
| 4ejnA | 1 | 0.5536 | 100 | 0.442 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)