| MSA PKC |
| ID: | 1497478885 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 672 (289) | ||
| Sequences: | 83765 (44792.7) | ||
| Seq/Len: | 289.844 | ||
| Nf(neff/√len): | 2634.9 |
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: 289.844).
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 |
| 444_A | 528_L | 3.425 | 1.00 |
| 470_M | 480_A | 3.387 | 1.00 |
| 355_L | 364_L | 3.331 | 1.00 |
| 574_T | 579_K | 3.327 | 1.00 |
| 343_M | 355_L | 3.118 | 1.00 |
| 344_V | 352_K | 2.894 | 1.00 |
| 452_F | 456_K | 2.727 | 1.00 |
| 358_R | 361_T | 2.690 | 1.00 |
| 356_A | 365_Y | 2.649 | 1.00 |
| 356_A | 367_I | 2.611 | 1.00 |
| 344_V | 347_K | 2.433 | 1.00 |
| 571_G | 581_L | 2.420 | 1.00 |
| 421_N | 473_S | 2.403 | 1.00 |
| 472_D | 476_H | 2.369 | 1.00 |
| 521_W | 572_L | 2.359 | 1.00 |
| 446_E | 476_H | 2.322 | 1.00 |
| 448_S | 524_Y | 2.308 | 1.00 |
| 451_L | 524_Y | 2.265 | 1.00 |
| 446_E | 477_I | 2.255 | 1.00 |
| 418_E | 478_K | 2.248 | 1.00 |
| 426_M | 467_D | 2.225 | 1.00 |
| 447_I | 469_V | 2.181 | 1.00 |
| 340_N | 357_D | 2.168 | 1.00 |
| 340_N | 359_K | 2.157 | 1.00 |
| 465_K | 501_T | 2.127 | 1.00 |
| 469_V | 477_I | 2.110 | 1.00 |
| 437_E | 562_S | 2.050 | 1.00 |
| 576_H | 579_K | 2.022 | 1.00 |
| 355_L | 419_Y | 2.013 | 1.00 |
| 357_D | 364_L | 1.998 | 1.00 |
| 344_V | 354_M | 1.957 | 1.00 |
| 450_G | 479_I | 1.938 | 1.00 |
| 342_L | 357_D | 1.914 | 1.00 |
| 506_A | 519_V | 1.900 | 1.00 |
| 567_S | 594_H | 1.875 | 1.00 |
| 436_K | 439_Q | 1.862 | 1.00 |
| 500_G | 505_I | 1.847 | 1.00 |
| 444_A | 524_Y | 1.840 | 1.00 |
| 384_T | 387_E | 1.766 | 1.00 |
| 424_D | 427_Y | 1.743 | 1.00 |
| 464_L | 527_L | 1.708 | 1.00 |
| 367_I | 416_V | 1.705 | 1.00 |
| 472_D | 478_K | 1.703 | 1.00 |
| 528_L | 568_V | 1.695 | 1.00 |
| 404_H | 418_E | 1.695 | 1.00 |
| 532_L | 565_A | 1.658 | 1.00 |
| 567_S | 571_G | 1.617 | 1.00 |
| 451_L | 464_L | 1.587 | 1.00 |
| 466_L | 504_Y | 1.583 | 1.00 |
| 440_A | 532_L | 1.581 | 1.00 |
| 347_K | 352_K | 1.581 | 1.00 |
| 338_D | 358_R | 1.522 | 1.00 |
| 399_F | 402_Q | 1.519 | 1.00 |
| 445_A | 449_I | 1.518 | 1.00 |
| 530_E | 536_P | 1.512 | 1.00 |
| 459_I | 485_C | 1.504 | 1.00 |
| 357_D | 362_E | 1.492 | 1.00 |
| 442_F | 446_E | 1.492 | 1.00 |
| 458_G | 517_K | 1.481 | 1.00 |
| 469_V | 527_L | 1.465 | 1.00 |
| 365_Y | 416_V | 1.460 | 1.00 |
| 568_V | 572_L | 1.434 | 1.00 |
| 354_M | 369_I | 1.433 | 1.00 |
| 426_M | 430_Q | 1.429 | 1.00 |
| 420_V | 478_K | 1.422 | 1.00 |
| 504_Y | 530_E | 1.410 | 1.00 |
| 420_V | 472_D | 1.409 | 1.00 |
| 401_T | 404_H | 1.401 | 0.99 |
| 342_L | 355_L | 1.394 | 0.99 |
| 402_Q | 418_E | 1.381 | 0.99 |
| 397_P | 453_F | 1.369 | 0.99 |
| 396_K | 399_F | 1.368 | 0.99 |
| 423_G | 431_Q | 1.353 | 0.99 |
| 453_F | 457_R | 1.350 | 0.99 |
| 461_Y | 464_L | 1.330 | 0.99 |
| 399_F | 404_H | 1.329 | 0.99 |
| 443_Y | 477_I | 1.325 | 0.99 |
| 396_K | 402_Q | 1.325 | 0.99 |
| 566_V | 570_K | 1.320 | 0.99 |
| 452_F | 592_R | 1.319 | 0.99 |
| 506_A | 509_I | 1.311 | 0.99 |
| 353_V | 366_A | 1.285 | 0.99 |
| 526_V | 536_P | 1.284 | 0.99 |
| 444_A | 531_M | 1.271 | 0.99 |
| 466_L | 527_L | 1.259 | 0.99 |
| 420_V | 470_M | 1.255 | 0.99 |
| 369_I | 414_Y | 1.254 | 0.99 |
| 509_I | 519_V | 1.246 | 0.98 |
| 553_H | 575_K | 1.244 | 0.98 |
| 447_I | 477_I | 1.244 | 0.98 |
| 426_M | 530_E | 1.242 | 0.98 |
| 449_I | 452_F | 1.221 | 0.98 |
| 403_L | 406_C | 1.213 | 0.98 |
| 369_I | 412_R | 1.213 | 0.98 |
| 451_L | 455_H | 1.210 | 0.98 |
| 364_L | 419_Y | 1.205 | 0.98 |
| 364_L | 421_N | 1.194 | 0.98 |
| 463_D | 468_N | 1.190 | 0.98 |
| 440_A | 531_M | 1.188 | 0.98 |
| 387_E | 391_L | 1.183 | 0.98 |
| 448_S | 591_V | 1.182 | 0.98 |
| 363_E | 404_H | 1.176 | 0.98 |
| 395_D | 402_Q | 1.173 | 0.98 |
| 388_K | 392_A | 1.167 | 0.97 |
| 358_R | 363_E | 1.164 | 0.97 |
| 341_F | 354_M | 1.160 | 0.97 |
| 397_P | 400_L | 1.159 | 0.97 |
| 568_V | 581_L | 1.153 | 0.97 |
| 437_E | 440_A | 1.148 | 0.97 |
| 348_G | 351_G | 1.147 | 0.97 |
| 571_G | 574_T | 1.144 | 0.97 |
| 484_M | 499_C | 1.140 | 0.97 |
| 432_V | 439_Q | 1.133 | 0.97 |
| 387_E | 390_V | 1.133 | 0.97 |
| 509_I | 515_Y | 1.132 | 0.97 |
| 462_R | 499_C | 1.123 | 0.97 |
| 342_L | 364_L | 1.117 | 0.96 |
| 548_Q | 552_E | 1.112 | 0.96 |
| 428_H | 432_V | 1.105 | 0.96 |
| 399_F | 450_G | 1.103 | 0.96 |
| 515_Y | 519_V | 1.100 | 0.96 |
| 367_I | 414_Y | 1.096 | 0.96 |
| 518_S | 582_G | 1.088 | 0.96 |
| 429_I | 530_E | 1.086 | 0.96 |
| 397_P | 401_T | 1.084 | 0.96 |
| 398_P | 401_T | 1.084 | 0.96 |
| 581_L | 590_D | 1.084 | 0.96 |
| 422_G | 475_G | 1.083 | 0.96 |
| 420_V | 480_A | 1.083 | 0.96 |
| 386_V | 389_R | 1.071 | 0.95 |
| 462_R | 515_Y | 1.070 | 0.95 |
| 466_L | 530_E | 1.068 | 0.95 |
| 557_Y | 566_V | 1.063 | 0.95 |
| 471_L | 477_I | 1.056 | 0.95 |
| 535_Q | 539_D | 1.055 | 0.95 |
| 569_C | 573_M | 1.054 | 0.95 |
| 454_L | 482_F | 1.051 | 0.94 |
| 525_G | 572_L | 1.044 | 0.94 |
| 447_I | 527_L | 1.038 | 0.94 |
| 563_K | 566_V | 1.032 | 0.94 |
| 468_N | 481_D | 1.030 | 0.94 |
| 345_L | 419_Y | 1.028 | 0.94 |
| 399_F | 449_I | 1.028 | 0.94 |
| 436_K | 440_A | 1.012 | 0.93 |
| 572_L | 581_L | 1.011 | 0.93 |
| 439_Q | 442_F | 1.007 | 0.93 |
| 389_R | 392_A | 1.006 | 0.93 |
| 428_H | 471_L | 1.005 | 0.93 |
| 442_F | 476_H | 1.000 | 0.92 |
| 574_T | 581_L | 1.000 | 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 | 0.172 | Contact Map |
| 2i0eA | 2 | 0.4851 | 100 | 0.582 | Contact Map |
| 3txoA | 1 | 0.4688 | 100 | 0.602 | Contact Map |
| 4dc2A | 1 | 0.4807 | 100 | 0.603 | Contact Map |
| 4gv1A | 1 | 0.4821 | 100 | 0.605 | Contact Map |
| 1xjdA | 1 | 0.4167 | 100 | 0.607 | Contact Map |
| 3a8xA | 2 | 0.4926 | 100 | 0.608 | Contact Map |
| 2r5tA | 1 | 0.4226 | 100 | 0.613 | Contact Map |
| 4othA | 1 | 0.4479 | 100 | 0.622 | Contact Map |
| 4aw2A | 1 | 0.567 | 100 | 0.624 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)