| Run for P6 and P7 |
| ID: | 1504735914 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 655 (602) | ||
| Sequences: | 9520 (8103.5) | ||
| Seq/Len: | 15.814 | ||
| Nf(neff/√len): | 330.3 |
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: 15.814).
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 |
| 473_R | 504_A | 4.015 | 1.00 |
| 268_V | 279_L | 3.289 | 1.00 |
| 163_S | 166_K | 3.231 | 1.00 |
| 511_A | 519_N | 2.851 | 1.00 |
| 417_Q | 615_P | 2.846 | 1.00 |
| 121_I | 150_L | 2.726 | 1.00 |
| 616_E | 620_S | 2.686 | 1.00 |
| 124_Q | 153_L | 2.666 | 1.00 |
| 108_A | 134_T | 2.562 | 1.00 |
| 446_A | 456_I | 2.550 | 1.00 |
| 136_N | 171_P | 2.535 | 1.00 |
| 134_T | 174_A | 2.534 | 1.00 |
| 464_T | 629_L | 2.522 | 1.00 |
| 114_L | 181_Q | 2.499 | 1.00 |
| 513_L | 633_L | 2.411 | 1.00 |
| 172_T | 175_E | 2.403 | 1.00 |
| 468_W | 625_A | 2.399 | 1.00 |
| 258_L | 362_L | 2.363 | 1.00 |
| 403_R | 523_Q | 2.362 | 1.00 |
| 485_P | 489_Q | 2.352 | 1.00 |
| 256_Q | 260_D | 2.339 | 1.00 |
| 118_M | 154_V | 2.336 | 1.00 |
| 137_Y | 142_G | 2.328 | 1.00 |
| 355_L | 494_V | 2.324 | 1.00 |
| 607_W | 619_L | 2.323 | 1.00 |
| 113_P | 116_T | 2.303 | 1.00 |
| 342_F | 347_F | 2.257 | 1.00 |
| 607_W | 623_F | 2.251 | 1.00 |
| 396_D | 530_H | 2.249 | 1.00 |
| 136_N | 139_E | 2.236 | 1.00 |
| 133_M | 173_I | 2.232 | 1.00 |
| 111_Q | 133_M | 2.211 | 1.00 |
| 255_W | 326_V | 2.202 | 1.00 |
| 596_V | 605_L | 2.199 | 1.00 |
| 132_G | 135_D | 2.198 | 1.00 |
| 122_W | 173_I | 2.195 | 1.00 |
| 459_T | 516_R | 2.187 | 1.00 |
| 462_A | 505_V | 2.151 | 1.00 |
| 258_L | 359_W | 2.140 | 1.00 |
| 251_I | 359_W | 2.138 | 1.00 |
| 76_L | 79_L | 2.130 | 1.00 |
| 442_L | 453_P | 2.114 | 1.00 |
| 268_V | 321_W | 2.112 | 1.00 |
| 166_K | 179_H | 2.112 | 1.00 |
| 357_S | 492_A | 2.095 | 1.00 |
| 475_T | 502_L | 2.052 | 1.00 |
| 261_H | 358_E | 2.034 | 1.00 |
| 522_Q | 526_R | 2.005 | 1.00 |
| 461_Y | 556_V | 1.994 | 1.00 |
| 428_E | 611_E | 1.988 | 1.00 |
| 473_R | 506_E | 1.978 | 1.00 |
| 257_R | 260_D | 1.977 | 1.00 |
| 449_F | 514_L | 1.977 | 1.00 |
| 252_N | 256_Q | 1.967 | 1.00 |
| 115_E | 133_M | 1.957 | 1.00 |
| 432_A | 605_L | 1.954 | 1.00 |
| 428_E | 616_E | 1.949 | 1.00 |
| 112_T | 133_M | 1.947 | 1.00 |
| 262_H | 358_E | 1.913 | 1.00 |
| 117_E | 120_A | 1.883 | 1.00 |
| 121_I | 154_V | 1.883 | 1.00 |
| 317_A | 320_V | 1.877 | 1.00 |
| 620_S | 624_A | 1.844 | 1.00 |
| 416_A | 618_M | 1.833 | 1.00 |
| 117_E | 157_R | 1.822 | 1.00 |
| 107_F | 130_R | 1.819 | 1.00 |
| 397_L | 541_E | 1.817 | 1.00 |
| 247_D | 250_R | 1.808 | 1.00 |
| 276_Q | 279_L | 1.806 | 1.00 |
| 627_C | 631_H | 1.792 | 1.00 |
| 398_D | 402_A | 1.788 | 1.00 |
| 396_D | 532_L | 1.782 | 1.00 |
| 138_F | 168_F | 1.774 | 1.00 |
| 514_L | 638_A | 1.765 | 1.00 |
| 170_K | 179_H | 1.761 | 1.00 |
| 461_Y | 594_H | 1.754 | 1.00 |
| 112_T | 181_Q | 1.748 | 1.00 |
| 636_E | 639_A | 1.748 | 1.00 |
| 466_G | 507_L | 1.746 | 1.00 |
| 430_L | 620_S | 1.733 | 1.00 |
| 438_K | 631_H | 1.732 | 1.00 |
| 455_G | 521_Q | 1.729 | 1.00 |
| 119_A | 173_I | 1.724 | 1.00 |
| 443_K | 598_E | 1.723 | 1.00 |
| 57_A | 73_F | 1.708 | 1.00 |
| 397_L | 533_V | 1.699 | 1.00 |
| 407_L | 475_T | 1.698 | 1.00 |
| 263_E | 376_S | 1.692 | 1.00 |
| 594_H | 607_W | 1.682 | 1.00 |
| 399_Y | 403_R | 1.673 | 1.00 |
| 512_T | 515_E | 1.669 | 1.00 |
| 155_R | 161_E | 1.655 | 1.00 |
| 108_A | 133_M | 1.655 | 1.00 |
| 118_M | 177_A | 1.650 | 1.00 |
| 112_T | 116_T | 1.643 | 1.00 |
| 461_Y | 558_F | 1.639 | 1.00 |
| 323_L | 346_I | 1.638 | 1.00 |
| 477_N | 554_M | 1.630 | 1.00 |
| 264_M | 267_A | 1.618 | 1.00 |
| 394_Q | 398_D | 1.613 | 1.00 |
| 59_F | 63_K | 1.610 | 1.00 |
| 116_T | 120_A | 1.599 | 1.00 |
| 625_A | 651_P | 1.598 | 1.00 |
| 537_T | 540_R | 1.583 | 1.00 |
| 247_D | 363_Y | 1.575 | 1.00 |
| 276_Q | 280_P | 1.566 | 1.00 |
| 114_L | 117_E | 1.562 | 1.00 |
| 248_L | 328_A | 1.558 | 1.00 |
| 535_G | 539_Q | 1.557 | 1.00 |
| 120_A | 157_R | 1.544 | 1.00 |
| 621_D | 625_A | 1.543 | 1.00 |
| 125_L | 150_L | 1.543 | 1.00 |
| 615_P | 618_M | 1.536 | 1.00 |
| 609_A | 619_L | 1.530 | 1.00 |
| 502_L | 538_V | 1.519 | 1.00 |
| 303_E | 306_A | 1.516 | 1.00 |
| 269_V | 346_I | 1.509 | 1.00 |
| 459_T | 520_L | 1.504 | 1.00 |
| 463_E | 629_L | 1.501 | 1.00 |
| 250_R | 363_Y | 1.501 | 1.00 |
| 401_T | 541_E | 1.475 | 1.00 |
| 251_I | 338_L | 1.471 | 1.00 |
| 403_R | 526_R | 1.468 | 1.00 |
| 291_D | 330_R | 1.466 | 1.00 |
| 444_E | 448_E | 1.464 | 1.00 |
| 397_L | 401_T | 1.463 | 1.00 |
| 257_R | 362_L | 1.463 | 1.00 |
| 538_V | 542_L | 1.458 | 1.00 |
| 435_D | 438_K | 1.447 | 1.00 |
| 119_A | 133_M | 1.443 | 1.00 |
| 143_D | 146_L | 1.443 | 1.00 |
| 424_S | 612_G | 1.441 | 1.00 |
| 225_S | 271_P | 1.438 | 1.00 |
| 118_M | 173_I | 1.438 | 1.00 |
| 150_L | 167_I | 1.437 | 1.00 |
| 57_A | 61_K | 1.426 | 1.00 |
| 453_P | 603_L | 1.418 | 1.00 |
| 460_A | 630_L | 1.416 | 1.00 |
| 468_W | 622_M | 1.415 | 1.00 |
| 441_K | 631_H | 1.414 | 1.00 |
| 326_V | 338_L | 1.413 | 1.00 |
| 214_T | 217_Q | 1.410 | 1.00 |
| 326_V | 340_I | 1.406 | 0.99 |
| 640_W | 643_T | 1.405 | 0.99 |
| 505_V | 520_L | 1.397 | 0.99 |
| 170_K | 175_E | 1.393 | 0.99 |
| 112_T | 115_E | 1.393 | 0.99 |
| 462_A | 476_I | 1.392 | 0.99 |
| 410_A | 550_Q | 1.388 | 0.99 |
| 399_Y | 527_D | 1.385 | 0.99 |
| 111_Q | 115_E | 1.385 | 0.99 |
| 463_E | 516_R | 1.384 | 0.99 |
| 458_L | 476_I | 1.382 | 0.99 |
| 167_I | 176_L | 1.379 | 0.99 |
| 426_R | 612_G | 1.377 | 0.99 |
| 277_Q | 280_P | 1.374 | 0.99 |
| 122_W | 142_G | 1.371 | 0.99 |
| 614_F | 619_L | 1.357 | 0.99 |
| 115_E | 177_A | 1.356 | 0.99 |
| 166_K | 169_D | 1.350 | 0.99 |
| 119_A | 131_V | 1.349 | 0.99 |
| 402_A | 405_D | 1.348 | 0.99 |
| 458_L | 524_L | 1.344 | 0.99 |
| 216_I | 219_A | 1.341 | 0.99 |
| 290_T | 327_R | 1.337 | 0.99 |
| 424_S | 610_V | 1.333 | 0.99 |
| 329_S | 339_H | 1.332 | 0.99 |
| 441_K | 635_E | 1.326 | 0.99 |
| 107_F | 132_G | 1.324 | 0.99 |
| 59_F | 62_H | 1.316 | 0.99 |
| 398_D | 401_T | 1.314 | 0.99 |
| 133_M | 174_A | 1.311 | 0.99 |
| 464_T | 626_Y | 1.308 | 0.99 |
| 460_A | 633_L | 1.302 | 0.99 |
| 433_K | 604_L | 1.297 | 0.99 |
| 231_G | 335_R | 1.295 | 0.99 |
| 377_F | 380_Y | 1.289 | 0.99 |
| 251_I | 363_Y | 1.288 | 0.99 |
| 52_N | 55_R | 1.280 | 0.99 |
| 88_D | 91_A | 1.278 | 0.99 |
| 632_R | 645_P | 1.274 | 0.99 |
| 117_E | 158_I | 1.273 | 0.99 |
| 246_L | 251_I | 1.272 | 0.99 |
| 558_F | 596_V | 1.271 | 0.99 |
| 160_V | 180_V | 1.264 | 0.99 |
| 114_L | 180_V | 1.261 | 0.99 |
| 108_A | 174_A | 1.261 | 0.99 |
| 165_G | 169_D | 1.259 | 0.99 |
| 537_T | 541_E | 1.252 | 0.99 |
| 311_M | 327_R | 1.250 | 0.99 |
| 347_F | 494_V | 1.250 | 0.99 |
| 547_G | 550_Q | 1.248 | 0.99 |
| 629_L | 644_A | 1.244 | 0.98 |
| 293_R | 333_D | 1.241 | 0.98 |
| 107_F | 110_P | 1.241 | 0.98 |
| 433_K | 602_E | 1.239 | 0.98 |
| 110_P | 133_M | 1.234 | 0.98 |
| 506_E | 511_A | 1.230 | 0.98 |
| 438_K | 441_K | 1.227 | 0.98 |
| 318_P | 345_L | 1.223 | 0.98 |
| 53_P | 73_F | 1.218 | 0.98 |
| 357_S | 361_R | 1.217 | 0.98 |
| 524_L | 528_L | 1.208 | 0.98 |
| 510_G | 642_E | 1.203 | 0.98 |
| 55_R | 59_F | 1.199 | 0.98 |
| 65_P | 68_M | 1.198 | 0.98 |
| 330_R | 336_V | 1.198 | 0.98 |
| 79_L | 87_V | 1.196 | 0.98 |
| 154_V | 180_V | 1.189 | 0.98 |
| 365_E | 368_A | 1.185 | 0.98 |
| 246_L | 336_V | 1.182 | 0.98 |
| 618_M | 621_D | 1.182 | 0.98 |
| 442_L | 456_I | 1.180 | 0.98 |
| 507_L | 511_A | 1.175 | 0.98 |
| 214_T | 377_F | 1.175 | 0.98 |
| 466_G | 469_S | 1.174 | 0.98 |
| 215_D | 384_L | 1.173 | 0.98 |
| 218_Q | 385_E | 1.173 | 0.98 |
| 111_Q | 174_A | 1.171 | 0.98 |
| 328_A | 338_L | 1.166 | 0.97 |
| 449_F | 518_R | 1.164 | 0.97 |
| 315_V | 325_D | 1.162 | 0.97 |
| 508_S | 511_A | 1.161 | 0.97 |
| 454_S | 478_L | 1.155 | 0.97 |
| 457_L | 560_S | 1.153 | 0.97 |
| 526_R | 529_D | 1.149 | 0.97 |
| 458_L | 558_F | 1.148 | 0.97 |
| 533_V | 541_E | 1.148 | 0.97 |
| 245_N | 334_G | 1.147 | 0.97 |
| 270_L | 277_Q | 1.141 | 0.97 |
| 122_W | 176_L | 1.141 | 0.97 |
| 220_Y | 496_D | 1.133 | 0.97 |
| 460_A | 626_Y | 1.133 | 0.97 |
| 439_W | 443_K | 1.129 | 0.97 |
| 441_K | 634_T | 1.128 | 0.97 |
| 451_L | 517_G | 1.126 | 0.97 |
| 267_A | 278_I | 1.123 | 0.97 |
| 248_L | 252_N | 1.122 | 0.97 |
| 457_L | 558_F | 1.120 | 0.96 |
| 311_M | 314_Q | 1.119 | 0.96 |
| 307_I | 329_S | 1.116 | 0.96 |
| 445_R | 449_F | 1.116 | 0.96 |
| 430_L | 616_E | 1.115 | 0.96 |
| 439_W | 453_P | 1.115 | 0.96 |
| 150_L | 176_L | 1.113 | 0.96 |
| 406_D | 504_A | 1.112 | 0.96 |
| 58_D | 62_H | 1.110 | 0.96 |
| 362_L | 370_L | 1.109 | 0.96 |
| 430_L | 623_F | 1.108 | 0.96 |
| 119_A | 123_C | 1.108 | 0.96 |
| 162_L | 176_L | 1.108 | 0.96 |
| 147_A | 164_L | 1.106 | 0.96 |
| 479_T | 559_T | 1.100 | 0.96 |
| 515_E | 518_R | 1.098 | 0.96 |
| 147_A | 167_I | 1.098 | 0.96 |
| 373_L | 493_L | 1.098 | 0.96 |
| 151_A | 167_I | 1.097 | 0.96 |
| 639_A | 643_T | 1.095 | 0.96 |
| 559_T | 562_L | 1.094 | 0.96 |
| 380_Y | 383_A | 1.090 | 0.96 |
| 432_A | 623_F | 1.089 | 0.96 |
| 263_E | 266_R | 1.088 | 0.96 |
| 324_F | 340_I | 1.088 | 0.96 |
| 465_L | 556_V | 1.086 | 0.96 |
| 435_D | 631_H | 1.085 | 0.96 |
| 347_F | 352_M | 1.084 | 0.96 |
| 350_W | 481_F | 1.083 | 0.96 |
| 351_S | 494_V | 1.082 | 0.96 |
| 533_V | 538_V | 1.081 | 0.95 |
| 252_N | 286_Q | 1.080 | 0.95 |
| 306_A | 310_E | 1.078 | 0.95 |
| 264_M | 494_V | 1.075 | 0.95 |
| 173_I | 176_L | 1.074 | 0.95 |
| 467_A | 625_A | 1.071 | 0.95 |
| 260_D | 281_Q | 1.069 | 0.95 |
| 222_L | 226_G | 1.065 | 0.95 |
| 149_R | 153_L | 1.060 | 0.95 |
| 259_I | 324_F | 1.060 | 0.95 |
| 451_L | 456_I | 1.058 | 0.95 |
| 480_Q | 501_T | 1.055 | 0.95 |
| 439_W | 603_L | 1.055 | 0.95 |
| 151_A | 155_R | 1.052 | 0.95 |
| 213_L | 217_Q | 1.052 | 0.95 |
| 279_L | 282_V | 1.050 | 0.94 |
| 342_F | 346_I | 1.050 | 0.94 |
| 472_S | 506_E | 1.049 | 0.94 |
| 128_V | 131_V | 1.045 | 0.94 |
| 519_N | 523_Q | 1.045 | 0.94 |
| 272_N | 275_Q | 1.044 | 0.94 |
| 254_A | 359_W | 1.044 | 0.94 |
| 118_M | 180_V | 1.039 | 0.94 |
| 457_L | 603_L | 1.038 | 0.94 |
| 594_H | 605_L | 1.037 | 0.94 |
| 394_Q | 397_L | 1.035 | 0.94 |
| 445_R | 634_T | 1.035 | 0.94 |
| 308_R | 339_H | 1.035 | 0.94 |
| 511_A | 515_E | 1.035 | 0.94 |
| 217_Q | 220_Y | 1.029 | 0.94 |
| 360_T | 364_H | 1.029 | 0.94 |
| 645_P | 652_R | 1.027 | 0.94 |
| 556_V | 559_T | 1.024 | 0.93 |
| 261_H | 362_L | 1.024 | 0.93 |
| 207_R | 263_E | 1.021 | 0.93 |
| 110_P | 119_A | 1.018 | 0.93 |
| 207_R | 211_F | 1.017 | 0.93 |
| 624_A | 627_C | 1.015 | 0.93 |
| 633_L | 644_A | 1.012 | 0.93 |
| 254_A | 362_L | 1.011 | 0.93 |
| 428_E | 609_A | 1.010 | 0.93 |
| 311_M | 341_S | 1.008 | 0.93 |
| 328_A | 336_V | 1.008 | 0.93 |
| 154_V | 160_V | 1.005 | 0.93 |
| 528_L | 531_P | 1.005 | 0.93 |
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 | |
| 2jgpA | 1 | 0.7878 | 100 | 0.298 | Contact Map |
| 4tx3B | 1 | 0.6718 | 100 | 0.473 | Contact Map |
| 2vsqA | 1 | 0.6733 | 100 | 0.478 | Contact Map |
| 1l5aA | 3 | 0.6427 | 100 | 0.483 | Contact Map |
| 4znmA | 2 | 0 | 100 | 0.497 | Contact Map |
| 4jn3A | 2 | 0.6489 | 100 | 0.497 | Contact Map |
| 4hvmA | 4 | 0.5863 | 100 | 0.509 | Contact Map |
| 2xhgA | 1 | 0.658 | 100 | 0.523 | Contact Map |
| 1q9jA | 2 | 0.5649 | 100 | 0.603 | Contact Map |
| 3fotA | 1 | 0.6687 | 100 | 0.634 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)