| BmrA |
| ID: | 1498479597 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 589 (572) | ||
| Sequences: | 42475 (29057.9) | ||
| Seq/Len: | 74.257 | ||
| Nf(neff/√len): | 1215.0 |
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: 74.257).
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 |
| 342_Q | 363_V | 4.705 | 1.00 |
| 345_R | 359_E | 4.501 | 1.00 |
| 458_L | 468_F | 4.419 | 1.00 |
| 365_E | 368_K | 4.404 | 1.00 |
| 368_K | 545_Q | 4.377 | 1.00 |
| 429_G | 433_E | 4.222 | 1.00 |
| 545_Q | 557_R | 4.173 | 1.00 |
| 344_D | 397_T | 4.119 | 1.00 |
| 453_E | 458_L | 4.103 | 1.00 |
| 340_P | 363_V | 4.036 | 1.00 |
| 344_D | 399_R | 3.863 | 1.00 |
| 432_R | 445_D | 3.634 | 1.00 |
| 458_L | 462_K | 3.464 | 1.00 |
| 397_T | 404_P | 3.445 | 1.00 |
| 432_R | 469_D | 3.426 | 1.00 |
| 560_H | 570_Y | 3.333 | 1.00 |
| 358_K | 553_E | 3.266 | 1.00 |
| 343_L | 346_V | 3.176 | 1.00 |
| 347_S | 359_E | 3.106 | 1.00 |
| 432_R | 436_C | 3.011 | 1.00 |
| 571_R | 575_E | 3.007 | 1.00 |
| 450_K | 454_M | 2.913 | 1.00 |
| 355_L | 358_K | 2.843 | 1.00 |
| 384_F | 501_M | 2.756 | 1.00 |
| 452_A | 468_F | 2.732 | 1.00 |
| 342_Q | 399_R | 2.728 | 1.00 |
| 416_H | 498_S | 2.714 | 1.00 |
| 384_F | 533_I | 2.621 | 1.00 |
| 340_P | 365_E | 2.615 | 1.00 |
| 445_D | 449_E | 2.600 | 1.00 |
| 443_V | 447_E | 2.560 | 1.00 |
| 435_I | 452_A | 2.548 | 1.00 |
| 567_H | 571_R | 2.517 | 1.00 |
| 449_E | 458_L | 2.506 | 1.00 |
| 364_I | 370_T | 2.479 | 1.00 |
| 496_N | 528_R | 2.459 | 1.00 |
| 432_R | 448_I | 2.451 | 1.00 |
| 558_G | 562_E | 2.450 | 1.00 |
| 559_T | 562_E | 2.442 | 1.00 |
| 347_S | 395_A | 2.433 | 1.00 |
| 547_L | 557_R | 2.409 | 1.00 |
| 466_N | 470_T | 2.390 | 1.00 |
| 409_S | 412_S | 2.382 | 1.00 |
| 347_S | 355_L | 2.373 | 1.00 |
| 362_A | 547_L | 2.358 | 1.00 |
| 349_G | 355_L | 2.319 | 1.00 |
| 449_E | 453_E | 2.288 | 1.00 |
| 389_R | 392_S | 2.272 | 1.00 |
| 157_T | 161_I | 2.247 | 1.00 |
| 340_P | 366_A | 2.240 | 1.00 |
| 418_G | 497_P | 2.230 | 1.00 |
| 439_L | 447_E | 2.171 | 1.00 |
| 392_S | 406_D | 2.150 | 1.00 |
| 550_E | 569_L | 2.127 | 1.00 |
| 343_L | 362_A | 2.117 | 1.00 |
| 522_E | 542_D | 2.113 | 1.00 |
| 556_G | 568_G | 2.084 | 1.00 |
| 349_G | 394_T | 2.053 | 1.00 |
| 447_E | 496_N | 2.047 | 1.00 |
| 369_V | 543_A | 2.034 | 1.00 |
| 451_A | 455_A | 2.013 | 1.00 |
| 550_E | 555_T | 1.993 | 1.00 |
| 457_A | 460_F | 1.986 | 1.00 |
| 345_R | 361_S | 1.979 | 1.00 |
| 556_G | 566_S | 1.976 | 1.00 |
| 370_T | 545_Q | 1.968 | 1.00 |
| 449_E | 462_K | 1.948 | 1.00 |
| 435_I | 448_I | 1.947 | 1.00 |
| 364_I | 531_I | 1.926 | 1.00 |
| 339_L | 401_G | 1.923 | 1.00 |
| 547_L | 554_I | 1.911 | 1.00 |
| 318_I | 322_A | 1.907 | 1.00 |
| 221_A | 224_V | 1.887 | 1.00 |
| 198_E | 235_S | 1.883 | 1.00 |
| 454_M | 523_V | 1.864 | 1.00 |
| 514_E | 536_R | 1.864 | 1.00 |
| 55_D | 281_G | 1.861 | 1.00 |
| 456_Y | 516_S | 1.855 | 1.00 |
| 371_A | 543_A | 1.847 | 1.00 |
| 370_T | 547_L | 1.833 | 1.00 |
| 368_K | 544_D | 1.829 | 1.00 |
| 17_A | 322_A | 1.824 | 1.00 |
| 383_L | 549_V | 1.802 | 1.00 |
| 515_K | 519_Q | 1.797 | 1.00 |
| 450_K | 453_E | 1.786 | 1.00 |
| 106_K | 325_E | 1.781 | 1.00 |
| 404_P | 407_T | 1.770 | 1.00 |
| 555_T | 569_L | 1.770 | 1.00 |
| 436_C | 448_I | 1.755 | 1.00 |
| 21_R | 102_L | 1.747 | 1.00 |
| 55_D | 279_T | 1.738 | 1.00 |
| 436_C | 445_D | 1.737 | 1.00 |
| 556_G | 567_H | 1.696 | 1.00 |
| 130_D | 316_R | 1.693 | 1.00 |
| 369_V | 532_V | 1.692 | 1.00 |
| 460_F | 483_Q | 1.669 | 1.00 |
| 445_D | 469_D | 1.651 | 1.00 |
| 372_I | 383_L | 1.639 | 1.00 |
| 452_A | 461_I | 1.606 | 1.00 |
| 341_I | 531_I | 1.595 | 1.00 |
| 340_P | 401_G | 1.589 | 1.00 |
| 338_H | 401_G | 1.586 | 1.00 |
| 267_G | 271_M | 1.581 | 1.00 |
| 357_L | 360_V | 1.576 | 1.00 |
| 447_E | 450_K | 1.567 | 1.00 |
| 365_E | 545_Q | 1.564 | 1.00 |
| 163_N | 272_Q | 1.553 | 1.00 |
| 459_N | 462_K | 1.550 | 1.00 |
| 388_E | 419_Y | 1.543 | 1.00 |
| 346_V | 393_P | 1.536 | 1.00 |
| 25_S | 98_G | 1.535 | 1.00 |
| 428_S | 471_E | 1.523 | 1.00 |
| 205_L | 232_G | 1.523 | 1.00 |
| 464_L | 470_T | 1.523 | 1.00 |
| 109_K | 325_E | 1.516 | 1.00 |
| 372_I | 547_L | 1.513 | 1.00 |
| 106_K | 110_L | 1.511 | 1.00 |
| 509_L | 517_V | 1.502 | 1.00 |
| 541_V | 561_H | 1.500 | 1.00 |
| 473_G | 478_M | 1.490 | 1.00 |
| 569_L | 572_D | 1.490 | 1.00 |
| 564_M | 574_A | 1.483 | 1.00 |
| 466_N | 471_E | 1.480 | 1.00 |
| 160_F | 167_T | 1.470 | 1.00 |
| 446_A | 449_E | 1.462 | 1.00 |
| 375_P | 550_E | 1.456 | 1.00 |
| 435_I | 494_L | 1.455 | 1.00 |
| 348_F | 386_L | 1.454 | 1.00 |
| 359_E | 553_E | 1.452 | 1.00 |
| 449_E | 468_F | 1.451 | 1.00 |
| 519_Q | 523_V | 1.447 | 1.00 |
| 452_A | 458_L | 1.445 | 1.00 |
| 386_L | 398_I | 1.443 | 1.00 |
| 217_K | 222_E | 1.426 | 1.00 |
| 454_M | 493_L | 1.419 | 1.00 |
| 201_R | 235_S | 1.413 | 1.00 |
| 343_L | 387_L | 1.409 | 1.00 |
| 347_S | 358_K | 1.406 | 0.99 |
| 446_A | 450_K | 1.404 | 0.99 |
| 193_R | 315_E | 1.402 | 0.99 |
| 418_G | 492_A | 1.395 | 0.99 |
| 348_F | 382_T | 1.387 | 0.99 |
| 534_A | 539_T | 1.381 | 0.99 |
| 387_L | 531_I | 1.380 | 0.99 |
| 472_V | 479_L | 1.363 | 0.99 |
| 187_K | 190_S | 1.355 | 0.99 |
| 371_A | 540_V | 1.353 | 0.99 |
| 362_A | 383_L | 1.351 | 0.99 |
| 271_M | 275_S | 1.339 | 0.99 |
| 344_D | 361_S | 1.337 | 0.99 |
| 68_G | 72_L | 1.329 | 0.99 |
| 198_E | 201_R | 1.323 | 0.99 |
| 447_E | 494_L | 1.323 | 0.99 |
| 198_E | 239_L | 1.320 | 0.99 |
| 348_F | 391_Y | 1.316 | 0.99 |
| 23_N | 26_Y | 1.313 | 0.99 |
| 360_V | 383_L | 1.307 | 0.99 |
| 556_G | 571_R | 1.294 | 0.99 |
| 339_L | 366_A | 1.288 | 0.99 |
| 337_A | 401_G | 1.284 | 0.99 |
| 431_I | 487_I | 1.283 | 0.99 |
| 343_L | 398_I | 1.280 | 0.99 |
| 194_E | 239_L | 1.268 | 0.99 |
| 443_V | 446_A | 1.263 | 0.99 |
| 561_H | 565_A | 1.262 | 0.99 |
| 343_L | 383_L | 1.262 | 0.99 |
| 455_A | 490_A | 1.254 | 0.99 |
| 118_N | 122_E | 1.253 | 0.99 |
| 209_I | 225_E | 1.250 | 0.99 |
| 106_K | 321_L | 1.240 | 0.98 |
| 355_L | 394_T | 1.237 | 0.98 |
| 451_A | 493_L | 1.235 | 0.98 |
| 105_K | 109_K | 1.234 | 0.98 |
| 420_V | 492_A | 1.231 | 0.98 |
| 457_A | 461_I | 1.231 | 0.98 |
| 375_P | 569_L | 1.210 | 0.98 |
| 479_L | 487_I | 1.210 | 0.98 |
| 279_T | 282_A | 1.204 | 0.98 |
| 212_E | 425_P | 1.203 | 0.98 |
| 393_P | 405_V | 1.200 | 0.98 |
| 403_E | 408_Y | 1.195 | 0.98 |
| 462_K | 467_Q | 1.191 | 0.98 |
| 523_V | 526_E | 1.185 | 0.98 |
| 386_L | 393_P | 1.183 | 0.98 |
| 424_S | 488_A | 1.182 | 0.98 |
| 51_K | 285_A | 1.179 | 0.98 |
| 452_A | 457_A | 1.179 | 0.98 |
| 485_Q | 507_S | 1.178 | 0.98 |
| 532_V | 543_A | 1.178 | 0.98 |
| 231_M | 235_S | 1.176 | 0.98 |
| 227_G | 231_M | 1.173 | 0.98 |
| 562_E | 566_S | 1.166 | 0.97 |
| 376_S | 513_S | 1.162 | 0.97 |
| 398_I | 405_V | 1.162 | 0.97 |
| 366_A | 498_S | 1.160 | 0.97 |
| 412_S | 415_E | 1.160 | 0.97 |
| 403_E | 407_T | 1.157 | 0.97 |
| 369_V | 530_T | 1.150 | 0.97 |
| 340_P | 402_D | 1.149 | 0.97 |
| 190_S | 194_E | 1.147 | 0.97 |
| 164_W | 168_L | 1.147 | 0.97 |
| 400_L | 413_W | 1.146 | 0.97 |
| 460_F | 464_L | 1.145 | 0.97 |
| 534_A | 540_V | 1.142 | 0.97 |
| 546_L | 560_H | 1.142 | 0.97 |
| 234_S | 238_K | 1.141 | 0.97 |
| 101_E | 105_K | 1.135 | 0.97 |
| 201_R | 232_G | 1.134 | 0.97 |
| 410_L | 414_R | 1.134 | 0.97 |
| 160_F | 164_W | 1.133 | 0.97 |
| 223_D | 227_G | 1.132 | 0.97 |
| 364_I | 529_T | 1.124 | 0.97 |
| 450_K | 496_N | 1.122 | 0.97 |
| 445_D | 448_I | 1.120 | 0.96 |
| 311_I | 315_E | 1.118 | 0.96 |
| 228_R | 232_G | 1.118 | 0.96 |
| 225_E | 437_Y | 1.117 | 0.96 |
| 119_A | 122_E | 1.117 | 0.96 |
| 103_L | 320_I | 1.117 | 0.96 |
| 370_T | 531_I | 1.117 | 0.96 |
| 268_Y | 272_Q | 1.113 | 0.96 |
| 388_E | 417_I | 1.113 | 0.96 |
| 463_E | 483_Q | 1.108 | 0.96 |
| 449_E | 452_A | 1.102 | 0.96 |
| 456_Y | 513_S | 1.100 | 0.96 |
| 360_V | 554_I | 1.097 | 0.96 |
| 237_F | 241_V | 1.095 | 0.96 |
| 378_G | 549_V | 1.094 | 0.96 |
| 24_P | 98_G | 1.092 | 0.96 |
| 525_M | 530_T | 1.091 | 0.96 |
| 98_G | 102_L | 1.091 | 0.96 |
| 388_E | 501_M | 1.087 | 0.96 |
| 179_L | 183_P | 1.085 | 0.96 |
| 389_R | 410_L | 1.081 | 0.95 |
| 338_H | 366_A | 1.081 | 0.95 |
| 342_Q | 402_D | 1.071 | 0.95 |
| 116_D | 385_K | 1.069 | 0.95 |
| 122_E | 200_A | 1.068 | 0.95 |
| 439_L | 442_D | 1.063 | 0.95 |
| 133_V | 313_A | 1.058 | 0.95 |
| 106_K | 109_K | 1.057 | 0.95 |
| 432_R | 449_E | 1.056 | 0.95 |
| 90_Y | 94_K | 1.054 | 0.95 |
| 432_R | 468_F | 1.053 | 0.95 |
| 166_L | 286_F | 1.050 | 0.94 |
| 400_L | 499_I | 1.048 | 0.94 |
| 194_E | 198_E | 1.045 | 0.94 |
| 116_D | 391_Y | 1.044 | 0.94 |
| 412_S | 416_H | 1.039 | 0.94 |
| 221_A | 225_E | 1.036 | 0.94 |
| 456_Y | 520_A | 1.034 | 0.94 |
| 159_L | 286_F | 1.031 | 0.94 |
| 498_S | 528_R | 1.029 | 0.94 |
| 346_V | 386_L | 1.026 | 0.94 |
| 349_G | 356_I | 1.026 | 0.94 |
| 473_G | 476_G | 1.024 | 0.93 |
| 342_Q | 361_S | 1.023 | 0.93 |
| 516_S | 519_Q | 1.022 | 0.93 |
| 248_S | 252_P | 1.021 | 0.93 |
| 173_V | 261_A | 1.017 | 0.93 |
| 224_V | 228_R | 1.015 | 0.93 |
| 235_S | 239_L | 1.015 | 0.93 |
| 454_M | 524_L | 1.014 | 0.93 |
| 560_H | 564_M | 1.010 | 0.93 |
| 371_A | 534_A | 1.009 | 0.93 |
| 272_Q | 277_E | 1.007 | 0.93 |
| 191_I | 242_R | 1.007 | 0.93 |
| 456_Y | 519_Q | 1.005 | 0.93 |
| 242_R | 245_K | 1.003 | 0.93 |
| 442_D | 494_L | 1.002 | 0.92 |
| 225_E | 228_R | 1.000 | 0.92 |
| 451_A | 494_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 | |
| 4ry2A | 2 | 0 | 100 | 0.056 | Contact Map |
| 4a82A | 4 | 0.9593 | 100 | 0.092 | Contact Map |
| 4q4hB | 1 | 0.9728 | 100 | 0.122 | Contact Map |
| 4f4cA | 1 | 0.9576 | 100 | 0.127 | Contact Map |
| 3b60A | 4 | 0.9626 | 100 | 0.133 | Contact Map |
| 3b5xA | 2 | 0.9626 | 100 | 0.136 | Contact Map |
| 3zdqA | 1 | 0.9423 | 100 | 0.143 | Contact Map |
| 4q9hA | 1 | 0.9643 | 100 | 0.146 | Contact Map |
| 4mrsA | 2 | 0.9864 | 100 | 0.147 | Contact Map |
| 4q4hA | 1 | 0.961 | 100 | 0.148 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)