| long_aln |
| ID: | 1420731923 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 476 (465) | ||
| Sequences: | 1730 (1443.4) | ||
| Seq/Len: | 3.720 | ||
| Nf(neff/√len): | 66.9 |
HHblits Results: (2013_03)
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: 3.720).
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 |
| 334_S | 376_I | 5.623 | 1.00 |
| 302_L | 381_L | 5.146 | 1.00 |
| 281_R | 285_I | 4.869 | 1.00 |
| 292_L | 388_F | 4.493 | 1.00 |
| 390_V | 425_M | 4.327 | 1.00 |
| 305_K | 372_V | 4.153 | 1.00 |
| 308_R | 371_A | 4.126 | 1.00 |
| 318_Q | 326_L | 3.176 | 1.00 |
| 302_L | 376_I | 3.126 | 1.00 |
| 397_L | 462_L | 3.113 | 1.00 |
| 316_G | 328_P | 3.067 | 1.00 |
| 318_Q | 328_P | 2.879 | 1.00 |
| 287_C | 397_L | 2.806 | 1.00 |
| 375_F | 379_T | 2.784 | 1.00 |
| 283_F | 287_C | 2.642 | 1.00 |
| 387_L | 397_L | 2.640 | 1.00 |
| 428_L | 432_S | 2.387 | 1.00 |
| 376_I | 381_L | 2.373 | 1.00 |
| 441_T | 444_Y | 2.343 | 1.00 |
| 291_I | 295_A | 2.315 | 1.00 |
| 95_V | 121_W | 2.297 | 1.00 |
| 338_N | 342_V | 2.261 | 1.00 |
| 387_L | 425_M | 2.208 | 1.00 |
| 307_T | 311_G | 2.193 | 1.00 |
| 301_Y | 305_K | 2.188 | 1.00 |
| 295_A | 299_M | 2.185 | 1.00 |
| 372_V | 376_I | 2.108 | 1.00 |
| 403_I | 439_Y | 2.100 | 1.00 |
| 320_V | 326_L | 2.051 | 1.00 |
| 303_W | 313_A | 2.051 | 1.00 |
| 407_E | 411_Y | 2.004 | 1.00 |
| 336_V | 342_V | 1.995 | 1.00 |
| 106_A | 114_R | 1.969 | 1.00 |
| 307_T | 313_A | 1.941 | 1.00 |
| 289_I | 391_L | 1.925 | 1.00 |
| 312_P | 337_M | 1.924 | 1.00 |
| 162_Y | 178_F | 1.911 | 1.00 |
| 288_S | 292_L | 1.875 | 1.00 |
| 376_I | 379_T | 1.852 | 1.00 |
| 404_V | 407_E | 1.840 | 1.00 |
| 403_I | 407_E | 1.826 | 0.99 |
| 411_Y | 439_Y | 1.813 | 0.99 |
| 36_V | 114_R | 1.806 | 0.99 |
| 365_N | 374_R | 1.763 | 0.99 |
| 149_T | 173_F | 1.760 | 0.99 |
| 314_I | 330_Y | 1.760 | 0.99 |
| 403_I | 411_Y | 1.715 | 0.99 |
| 146_K | 174_D | 1.676 | 0.99 |
| 345_E | 349_N | 1.671 | 0.99 |
| 364_K | 476_Y | 1.666 | 0.99 |
| 330_Y | 392_K | 1.661 | 0.99 |
| 143_G | 172_G | 1.661 | 0.99 |
| 369_I | 374_R | 1.656 | 0.99 |
| 371_A | 374_R | 1.655 | 0.99 |
| 330_Y | 389_N | 1.654 | 0.99 |
| 155_G | 158_A | 1.652 | 0.99 |
| 86_E | 136_K | 1.645 | 0.99 |
| 380_S | 434_R | 1.623 | 0.98 |
| 321_G | 423_P | 1.623 | 0.98 |
| 271_L | 418_Y | 1.619 | 0.98 |
| 151_I | 158_A | 1.607 | 0.98 |
| 428_L | 445_F | 1.607 | 0.98 |
| 296_S | 299_M | 1.605 | 0.98 |
| 404_V | 439_Y | 1.589 | 0.98 |
| 210_H | 239_T | 1.583 | 0.98 |
| 284_D | 396_S | 1.579 | 0.98 |
| 388_F | 394_D | 1.578 | 0.98 |
| 299_M | 314_I | 1.577 | 0.98 |
| 177_A | 195_K | 1.575 | 0.98 |
| 380_S | 453_W | 1.568 | 0.98 |
| 256_F | 261_E | 1.561 | 0.98 |
| 109_K | 114_R | 1.542 | 0.98 |
| 460_A | 464_K | 1.537 | 0.98 |
| 281_R | 288_S | 1.530 | 0.98 |
| 151_I | 178_F | 1.528 | 0.98 |
| 285_I | 288_S | 1.527 | 0.98 |
| 291_I | 397_L | 1.524 | 0.97 |
| 448_W | 452_N | 1.507 | 0.97 |
| 299_M | 332_F | 1.503 | 0.97 |
| 288_S | 391_L | 1.498 | 0.97 |
| 158_A | 178_F | 1.495 | 0.97 |
| 361_F | 403_I | 1.487 | 0.97 |
| 403_I | 442_R | 1.470 | 0.97 |
| 429_W | 435_N | 1.464 | 0.97 |
| 296_S | 300_I | 1.458 | 0.96 |
| 384_L | 387_L | 1.456 | 0.96 |
| 434_R | 453_W | 1.454 | 0.96 |
| 292_L | 296_S | 1.451 | 0.96 |
| 398_V | 462_L | 1.449 | 0.96 |
| 316_G | 330_Y | 1.437 | 0.96 |
| 387_L | 462_L | 1.436 | 0.96 |
| 403_I | 443_V | 1.436 | 0.96 |
| 302_L | 332_F | 1.434 | 0.96 |
| 346_L | 361_F | 1.432 | 0.96 |
| 455_L | 459_I | 1.423 | 0.96 |
| 315_Y | 404_V | 1.415 | 0.96 |
| 179_F | 205_R | 1.414 | 0.96 |
| 388_F | 392_K | 1.413 | 0.96 |
| 283_F | 455_L | 1.408 | 0.95 |
| 469_V | 474_G | 1.406 | 0.95 |
| 342_V | 345_E | 1.405 | 0.95 |
| 148_K | 174_D | 1.398 | 0.95 |
| 403_I | 418_Y | 1.397 | 0.95 |
| 403_I | 429_W | 1.392 | 0.95 |
| 338_N | 341_E | 1.388 | 0.95 |
| 315_Y | 340_Q | 1.362 | 0.94 |
| 318_Q | 406_D | 1.352 | 0.94 |
| 398_V | 426_T | 1.351 | 0.94 |
| 362_K | 429_W | 1.351 | 0.94 |
| 464_K | 468_V | 1.350 | 0.94 |
| 397_L | 425_M | 1.336 | 0.94 |
| 411_Y | 443_V | 1.328 | 0.93 |
| 407_E | 439_Y | 1.328 | 0.93 |
| 433_G | 437_V | 1.321 | 0.93 |
| 418_Y | 442_R | 1.319 | 0.93 |
| 154_S | 158_A | 1.315 | 0.93 |
| 403_I | 408_L | 1.308 | 0.93 |
| 150_I | 179_F | 1.299 | 0.92 |
| 320_V | 408_L | 1.289 | 0.92 |
| 404_V | 408_L | 1.275 | 0.91 |
| 299_M | 384_L | 1.265 | 0.91 |
| 380_S | 442_R | 1.259 | 0.91 |
| 408_L | 411_Y | 1.246 | 0.90 |
| 32_S | 36_V | 1.245 | 0.90 |
| 299_M | 302_L | 1.242 | 0.90 |
| 435_N | 442_R | 1.230 | 0.89 |
| 362_K | 439_Y | 1.221 | 0.89 |
| 405_S | 409_E | 1.219 | 0.89 |
| 151_I | 155_G | 1.217 | 0.89 |
| 291_I | 387_L | 1.212 | 0.88 |
| 433_G | 453_W | 1.210 | 0.88 |
| 280_K | 284_D | 1.208 | 0.88 |
| 20_S | 131_F | 1.206 | 0.88 |
| 285_I | 387_L | 1.199 | 0.88 |
| 336_V | 367_P | 1.195 | 0.87 |
| 346_L | 350_D | 1.194 | 0.87 |
| 285_I | 289_I | 1.192 | 0.87 |
| 70_F | 76_H | 1.187 | 0.87 |
| 283_F | 459_I | 1.182 | 0.87 |
| 109_K | 113_S | 1.181 | 0.86 |
| 429_W | 445_F | 1.179 | 0.86 |
| 297_P | 300_I | 1.176 | 0.86 |
| 403_I | 406_D | 1.170 | 0.86 |
| 300_I | 304_Y | 1.164 | 0.85 |
| 317_H | 340_Q | 1.162 | 0.85 |
| 98_A | 121_W | 1.152 | 0.85 |
| 362_K | 407_E | 1.152 | 0.85 |
| 404_V | 411_Y | 1.145 | 0.84 |
| 378_K | 472_R | 1.134 | 0.83 |
| 411_Y | 418_Y | 1.128 | 0.83 |
| 469_V | 472_R | 1.128 | 0.83 |
| 24_F | 28_A | 1.124 | 0.83 |
| 28_A | 32_S | 1.124 | 0.83 |
| 329_C | 408_L | 1.123 | 0.82 |
| 308_R | 376_I | 1.120 | 0.82 |
| 196_D | 200_I | 1.120 | 0.82 |
| 21_D | 28_A | 1.120 | 0.82 |
| 361_F | 442_R | 1.118 | 0.82 |
| 439_Y | 442_R | 1.117 | 0.82 |
| 406_D | 411_Y | 1.105 | 0.81 |
| 317_H | 404_V | 1.099 | 0.81 |
| 363_L | 429_W | 1.099 | 0.81 |
| 403_I | 415_V | 1.097 | 0.80 |
| 158_A | 180_D | 1.094 | 0.80 |
| 317_H | 403_I | 1.092 | 0.80 |
| 429_W | 439_Y | 1.087 | 0.80 |
| 151_I | 162_Y | 1.078 | 0.79 |
| 298_L | 302_L | 1.076 | 0.79 |
| 434_R | 442_R | 1.076 | 0.79 |
| 162_Y | 193_V | 1.075 | 0.78 |
| 140_N | 145_W | 1.075 | 0.78 |
| 324_G | 419_L | 1.073 | 0.78 |
| 437_V | 442_R | 1.072 | 0.78 |
| 360_D | 403_I | 1.070 | 0.78 |
| 306_V | 381_L | 1.069 | 0.78 |
| 154_S | 180_D | 1.067 | 0.78 |
| 351_P | 358_E | 1.066 | 0.78 |
| 415_V | 418_Y | 1.066 | 0.78 |
| 343_L | 403_I | 1.062 | 0.77 |
| 467_K | 473_D | 1.054 | 0.77 |
| 428_L | 457_N | 1.050 | 0.76 |
| 202_D | 206_T | 1.046 | 0.76 |
| 151_I | 214_A | 1.045 | 0.76 |
| 403_I | 419_L | 1.045 | 0.76 |
| 418_Y | 439_Y | 1.040 | 0.75 |
| 153_G | 212_I | 1.039 | 0.75 |
| 357_W | 403_I | 1.038 | 0.75 |
| 285_I | 391_L | 1.037 | 0.75 |
| 289_I | 293_I | 1.036 | 0.75 |
| 336_V | 339_S | 1.027 | 0.74 |
| 360_D | 439_Y | 1.019 | 0.73 |
| 327_F | 395_M | 1.018 | 0.73 |
| 28_A | 127_L | 1.015 | 0.73 |
| 361_F | 435_N | 1.012 | 0.72 |
| 361_F | 404_V | 1.009 | 0.72 |
| 320_V | 361_F | 1.009 | 0.72 |
| 362_K | 403_I | 1.007 | 0.72 |
| 408_L | 419_L | 1.005 | 0.72 |
| 407_E | 419_L | 1.004 | 0.71 |
| 463_F | 467_K | 1.002 | 0.71 |
| 417_Y | 451_K | 1.002 | 0.71 |
| 404_V | 443_V | 1.001 | 0.71 |
| 350_D | 353_A | 1.001 | 0.71 |
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 | |
| 3nklA | 2 | 0.2479 | 99 | 0.915 | Contact Map |
| 2py6A | 1 | 0.4916 | 96.1 | 0.953 | Contact Map |
| 3wg9A | 4 | 0.416 | 92.1 | 0.961 | Contact Map |
| 4ea9A | 1 | 0.4097 | 92 | 0.961 | Contact Map |
| 3keoA | 2 | 0.4118 | 90.6 | 0.963 | Contact Map |
| 2vt3A | 2 | 0.4076 | 89.9 | 0.963 | Contact Map |
| 2dt5A | 2 | 0.4097 | 87.2 | 0.965 | Contact Map |
| 4m98A | 1 | 0.4286 | 77.2 | 0.969 | Contact Map |
| 3ff4A | 1 | 0.2437 | 58.7 | 0.972 | Contact Map |
| 2g6tA | 2 | 0.4874 | 55.7 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)