| cdc20 |
| ID: | 1452594870 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 499 (245) | ||
| Sequences: | 7488 (5570.7) | ||
| Seq/Len: | 30.563 | ||
| Nf(neff/√len): | 355.9 |
Jackhmmer Results: (2015_08)
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: 30.563).
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 |
| 392_C | 435_K | 3.409 | 1.00 |
| 388_C | 431_P | 3.158 | 1.00 |
| 339_A | 388_C | 2.869 | 1.00 |
| 391_A | 434_A | 2.846 | 1.00 |
| 339_A | 431_P | 2.745 | 1.00 |
| 412_K | 456_A | 2.606 | 1.00 |
| 413_E | 457_T | 2.566 | 1.00 |
| 342_E | 391_A | 2.558 | 1.00 |
| 394_S | 437_A | 2.444 | 1.00 |
| 347_P | 392_C | 2.417 | 1.00 |
| 323_H | 457_T | 2.263 | 1.00 |
| 322_R | 456_A | 2.249 | 1.00 |
| 322_R | 412_K | 2.232 | 1.00 |
| 317_W | 363_W | 2.228 | 1.00 |
| 372_A | 375_G | 2.184 | 1.00 |
| 323_H | 413_E | 2.139 | 1.00 |
| 393_L | 436_V | 2.139 | 1.00 |
| 397_D | 440_K | 2.134 | 1.00 |
| 316_R | 362_A | 2.039 | 1.00 |
| 349_Q | 394_S | 2.020 | 1.00 |
| 362_A | 406_L | 1.972 | 1.00 |
| 406_L | 450_T | 1.959 | 1.00 |
| 342_E | 434_A | 1.940 | 1.00 |
| 407_W | 451_M | 1.928 | 1.00 |
| 343_G | 392_C | 1.899 | 1.00 |
| 363_W | 451_M | 1.869 | 1.00 |
| 309_S | 355_Q | 1.838 | 1.00 |
| 343_G | 435_K | 1.833 | 1.00 |
| 425_L | 460_S | 1.830 | 1.00 |
| 363_W | 407_W | 1.788 | 1.00 |
| 309_S | 443_T | 1.756 | 1.00 |
| 447_L | 463_A | 1.752 | 1.00 |
| 313_C | 329_N | 1.741 | 1.00 |
| 383_R | 395_A | 1.729 | 1.00 |
| 340_P | 389_S | 1.723 | 1.00 |
| 387_V | 430_Y | 1.699 | 1.00 |
| 389_S | 432_T | 1.694 | 1.00 |
| 362_A | 450_T | 1.690 | 1.00 |
| 322_R | 368_S | 1.655 | 1.00 |
| 368_S | 412_K | 1.650 | 1.00 |
| 349_Q | 437_A | 1.649 | 1.00 |
| 337_P | 386_N | 1.639 | 1.00 |
| 306_S | 352_T | 1.620 | 1.00 |
| 306_S | 397_D | 1.608 | 1.00 |
| 317_W | 407_W | 1.608 | 1.00 |
| 395_A | 438_E | 1.600 | 1.00 |
| 355_Q | 443_T | 1.595 | 1.00 |
| 352_T | 397_D | 1.570 | 1.00 |
| 338_S | 387_V | 1.570 | 1.00 |
| 316_R | 450_T | 1.565 | 1.00 |
| 403_C | 447_L | 1.560 | 1.00 |
| 386_N | 429_K | 1.560 | 1.00 |
| 317_W | 451_M | 1.540 | 1.00 |
| 303_A | 349_Q | 1.532 | 1.00 |
| 313_C | 359_K | 1.527 | 1.00 |
| 314_G | 327_G | 1.527 | 1.00 |
| 316_R | 406_L | 1.517 | 1.00 |
| 359_K | 403_C | 1.509 | 1.00 |
| 382_I | 416_S | 1.489 | 1.00 |
| 359_K | 378_S | 1.475 | 1.00 |
| 400_S | 443_T | 1.471 | 1.00 |
| 338_S | 430_Y | 1.470 | 1.00 |
| 347_P | 435_K | 1.457 | 1.00 |
| 368_S | 456_A | 1.432 | 1.00 |
| 352_T | 440_K | 1.399 | 0.99 |
| 306_S | 440_K | 1.398 | 0.99 |
| 348_L | 393_L | 1.389 | 0.99 |
| 442_H | 460_S | 1.388 | 0.99 |
| 448_S | 461_A | 1.373 | 0.99 |
| 331_N | 380_R | 1.372 | 0.99 |
| 429_K | 471_R | 1.369 | 0.99 |
| 355_Q | 400_S | 1.358 | 0.99 |
| 313_C | 403_C | 1.338 | 0.99 |
| 340_P | 432_T | 1.291 | 0.99 |
| 415_I | 451_M | 1.291 | 0.99 |
| 380_R | 423_N | 1.289 | 0.99 |
| 370_V | 413_E | 1.287 | 0.99 |
| 409_P | 455_G | 1.287 | 0.99 |
| 328_G | 332_L | 1.277 | 0.99 |
| 365_P | 411_Y | 1.275 | 0.99 |
| 337_P | 429_K | 1.273 | 0.99 |
| 323_H | 370_V | 1.268 | 0.99 |
| 366_W | 369_N | 1.257 | 0.99 |
| 313_C | 447_L | 1.245 | 0.98 |
| 303_A | 394_S | 1.233 | 0.98 |
| 318_A | 363_W | 1.223 | 0.98 |
| 357_A | 445_R | 1.209 | 0.98 |
| 334_N | 350_T | 1.205 | 0.98 |
| 359_K | 447_L | 1.203 | 0.98 |
| 325_A | 363_W | 1.201 | 0.98 |
| 282_S | 292_H | 1.198 | 0.98 |
| 308_H | 326_S | 1.197 | 0.98 |
| 347_P | 350_T | 1.191 | 0.98 |
| 384_I | 427_I | 1.177 | 0.98 |
| 348_L | 436_V | 1.170 | 0.97 |
| 423_N | 465_E | 1.169 | 0.97 |
| 408_S | 451_M | 1.164 | 0.97 |
| 314_G | 360_A | 1.159 | 0.97 |
| 334_N | 383_R | 1.158 | 0.97 |
| 323_H | 369_N | 1.150 | 0.97 |
| 333_V | 382_I | 1.148 | 0.97 |
| 427_I | 469_L | 1.146 | 0.97 |
| 311_E | 357_A | 1.134 | 0.97 |
| 337_P | 340_P | 1.125 | 0.97 |
| 303_A | 437_A | 1.118 | 0.96 |
| 354_H | 358_V | 1.105 | 0.96 |
| 404_S | 448_S | 1.104 | 0.96 |
| 426_V | 438_E | 1.103 | 0.96 |
| 409_P | 453_P | 1.098 | 0.96 |
| 324_L | 458_V | 1.096 | 0.96 |
| 323_H | 335_V | 1.093 | 0.96 |
| 426_V | 468_R | 1.090 | 0.96 |
| 415_I | 458_V | 1.088 | 0.96 |
| 370_V | 457_T | 1.078 | 0.95 |
| 435_K | 438_E | 1.074 | 0.95 |
| 383_R | 392_C | 1.065 | 0.95 |
| 335_V | 427_I | 1.062 | 0.95 |
| 370_V | 373_T | 1.056 | 0.95 |
| 329_N | 378_S | 1.056 | 0.95 |
| 335_V | 384_I | 1.046 | 0.94 |
| 314_G | 448_S | 1.038 | 0.94 |
| 360_A | 404_S | 1.038 | 0.94 |
| 457_T | 469_L | 1.037 | 0.94 |
| 331_N | 423_N | 1.032 | 0.94 |
| 419_G | 423_N | 1.031 | 0.94 |
| 429_K | 432_T | 1.029 | 0.94 |
| 369_N | 413_E | 1.026 | 0.94 |
| 256_Q | 296_R | 1.024 | 0.93 |
| 324_L | 414_L | 1.021 | 0.93 |
| 384_I | 469_L | 1.004 | 0.93 |
| 382_I | 425_L | 1.002 | 0.92 |
| 335_V | 469_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 | |
| 4ggaA | 1 | 0.6293 | 100 | 0.473 | Contact Map |
| 4aezA | 3 | 0.6493 | 100 | 0.518 | Contact Map |
| 4ui9R | 1 | 0 | 100 | 0.553 | Contact Map |
| 4bh6A | 8 | 0.6112 | 100 | 0.559 | Contact Map |
| 4ggcA | 1 | 0.6273 | 100 | 0.566 | Contact Map |
| 1vyhC | 10 | 0.5852 | 100 | 0.656 | Contact Map |
| 4wjuA | 2 | 0.7054 | 100 | 0.669 | Contact Map |
| 3w15A | 1 | 0.5731 | 100 | 0.674 | Contact Map |
| 1gotB | 1 | 0.6593 | 100 | 0.677 | Contact Map |
| 4u1eI | 1 | 0.6152 | 100 | 0.682 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)