| M-2 |
| ID: | 1481208897 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 524 (465) | ||
| Sequences: | 14116 (8127.3) | ||
| Seq/Len: | 30.357 | ||
| Nf(neff/√len): | 376.9 |
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: 30.357).
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 |
| 232_K | 235_E | 7.189 | 1.00 |
| 132_D | 136_G | 4.653 | 1.00 |
| 233_H | 262_K | 4.618 | 1.00 |
| 364_G | 401_F | 4.475 | 1.00 |
| 237_L | 255_Q | 4.227 | 1.00 |
| 123_V | 127_T | 3.812 | 1.00 |
| 129_K | 133_T | 3.764 | 1.00 |
| 366_C | 469_A | 3.314 | 1.00 |
| 363_G | 472_F | 3.276 | 1.00 |
| 341_V | 400_I | 2.913 | 1.00 |
| 361_S | 405_A | 2.790 | 1.00 |
| 233_H | 237_L | 2.666 | 1.00 |
| 124_L | 137_G | 2.571 | 1.00 |
| 228_I | 233_H | 2.550 | 1.00 |
| 359_L | 472_F | 2.457 | 1.00 |
| 418_L | 426_G | 2.384 | 1.00 |
| 185_W | 332_A | 2.236 | 1.00 |
| 298_F | 302_W | 2.234 | 1.00 |
| 126_A | 204_L | 2.191 | 1.00 |
| 299_F | 471_E | 2.184 | 1.00 |
| 114_G | 147_L | 2.168 | 1.00 |
| 92_I | 432_M | 2.147 | 1.00 |
| 197_W | 201_I | 2.120 | 1.00 |
| 370_V | 465_T | 2.114 | 1.00 |
| 130_N | 133_T | 2.113 | 1.00 |
| 237_L | 258_F | 2.105 | 1.00 |
| 166_A | 350_D | 2.099 | 1.00 |
| 355_R | 476_F | 2.048 | 1.00 |
| 359_L | 476_F | 2.045 | 1.00 |
| 485_P | 489_E | 2.032 | 1.00 |
| 127_T | 133_T | 2.016 | 1.00 |
| 389_K | 393_F | 1.982 | 1.00 |
| 101_L | 110_P | 1.959 | 1.00 |
| 298_F | 437_A | 1.933 | 1.00 |
| 112_I | 217_I | 1.914 | 1.00 |
| 343_V | 347_L | 1.890 | 1.00 |
| 362_T | 472_F | 1.857 | 1.00 |
| 128_A | 133_T | 1.853 | 1.00 |
| 112_I | 214_L | 1.850 | 1.00 |
| 237_L | 241_A | 1.838 | 1.00 |
| 368_T | 394_F | 1.833 | 1.00 |
| 201_I | 205_L | 1.824 | 1.00 |
| 90_G | 139_T | 1.796 | 1.00 |
| 61_S | 187_A | 1.782 | 1.00 |
| 181_L | 336_G | 1.779 | 1.00 |
| 278_L | 282_K | 1.775 | 1.00 |
| 188_F | 329_G | 1.758 | 1.00 |
| 105_F | 109_T | 1.753 | 1.00 |
| 444_A | 464_Y | 1.747 | 1.00 |
| 393_F | 397_V | 1.742 | 1.00 |
| 413_Y | 479_Y | 1.733 | 1.00 |
| 462_L | 466_C | 1.704 | 1.00 |
| 440_L | 444_A | 1.686 | 1.00 |
| 362_T | 406_W | 1.683 | 1.00 |
| 348_L | 352_L | 1.668 | 1.00 |
| 102_T | 151_A | 1.649 | 1.00 |
| 44_I | 216_G | 1.646 | 1.00 |
| 244_H | 257_E | 1.645 | 1.00 |
| 486_T | 489_E | 1.641 | 1.00 |
| 226_F | 230_K | 1.640 | 1.00 |
| 103_D | 424_G | 1.639 | 1.00 |
| 279_D | 282_K | 1.636 | 1.00 |
| 279_D | 421_R | 1.636 | 1.00 |
| 295_S | 474_F | 1.627 | 1.00 |
| 355_R | 359_L | 1.626 | 1.00 |
| 108_K | 112_I | 1.623 | 1.00 |
| 386_G | 390_A | 1.611 | 1.00 |
| 124_L | 133_T | 1.607 | 1.00 |
| 448_A | 463_I | 1.594 | 1.00 |
| 287_R | 291_A | 1.584 | 1.00 |
| 109_T | 112_I | 1.571 | 1.00 |
| 475_V | 479_Y | 1.558 | 1.00 |
| 125_Q | 137_G | 1.555 | 1.00 |
| 474_F | 478_M | 1.553 | 1.00 |
| 86_L | 135_M | 1.548 | 1.00 |
| 350_D | 353_G | 1.547 | 1.00 |
| 294_L | 429_V | 1.541 | 1.00 |
| 238_H | 242_K | 1.540 | 1.00 |
| 255_Q | 259_R | 1.534 | 1.00 |
| 185_W | 189_G | 1.528 | 1.00 |
| 469_A | 473_V | 1.526 | 1.00 |
| 197_W | 204_L | 1.517 | 1.00 |
| 295_S | 299_F | 1.514 | 1.00 |
| 294_L | 433_S | 1.512 | 1.00 |
| 160_A | 168_L | 1.495 | 1.00 |
| 262_K | 266_R | 1.491 | 1.00 |
| 234_D | 238_H | 1.490 | 1.00 |
| 370_V | 374_L | 1.489 | 1.00 |
| 373_T | 462_L | 1.475 | 1.00 |
| 98_V | 147_L | 1.465 | 1.00 |
| 228_I | 236_A | 1.464 | 1.00 |
| 374_L | 378_L | 1.463 | 1.00 |
| 227_L | 232_K | 1.456 | 1.00 |
| 83_L | 131_L | 1.455 | 1.00 |
| 121_G | 140_M | 1.450 | 1.00 |
| 90_G | 94_S | 1.449 | 1.00 |
| 240_L | 261_I | 1.444 | 1.00 |
| 302_W | 437_A | 1.439 | 1.00 |
| 103_D | 107_R | 1.438 | 1.00 |
| 225_R | 488_E | 1.436 | 1.00 |
| 293_L | 418_L | 1.433 | 1.00 |
| 354_R | 416_E | 1.428 | 1.00 |
| 390_A | 394_F | 1.421 | 1.00 |
| 119_I | 214_L | 1.420 | 1.00 |
| 235_E | 238_H | 1.413 | 1.00 |
| 366_C | 370_V | 1.413 | 1.00 |
| 131_L | 135_M | 1.407 | 0.99 |
| 86_L | 139_T | 1.406 | 0.99 |
| 312_S | 316_Y | 1.391 | 0.99 |
| 48_A | 152_S | 1.385 | 0.99 |
| 259_R | 262_K | 1.385 | 0.99 |
| 276_S | 279_D | 1.384 | 0.99 |
| 121_G | 137_G | 1.384 | 0.99 |
| 258_F | 262_K | 1.371 | 0.99 |
| 227_L | 239_I | 1.370 | 0.99 |
| 485_P | 493_V | 1.367 | 0.99 |
| 359_L | 475_V | 1.365 | 0.99 |
| 352_L | 360_A | 1.362 | 0.99 |
| 338_A | 403_S | 1.362 | 0.99 |
| 50_A | 182_V | 1.358 | 0.99 |
| 356_L | 360_A | 1.353 | 0.99 |
| 177_N | 338_A | 1.347 | 0.99 |
| 103_D | 425_K | 1.344 | 0.99 |
| 359_L | 363_G | 1.344 | 0.99 |
| 303_S | 468_I | 1.340 | 0.99 |
| 259_R | 263_E | 1.338 | 0.99 |
| 185_W | 188_F | 1.338 | 0.99 |
| 366_C | 472_F | 1.336 | 0.99 |
| 227_L | 235_E | 1.329 | 0.99 |
| 353_G | 483_K | 1.328 | 0.99 |
| 413_Y | 417_I | 1.325 | 0.99 |
| 115_C | 214_L | 1.321 | 0.99 |
| 119_I | 210_S | 1.310 | 0.99 |
| 452_F | 463_I | 1.309 | 0.99 |
| 444_A | 447_V | 1.309 | 0.99 |
| 353_G | 356_L | 1.307 | 0.99 |
| 293_L | 430_M | 1.304 | 0.99 |
| 184_S | 335_T | 1.293 | 0.99 |
| 371_I | 375_T | 1.290 | 0.99 |
| 126_A | 207_A | 1.290 | 0.99 |
| 233_H | 258_F | 1.290 | 0.99 |
| 225_R | 487_L | 1.289 | 0.99 |
| 223_S | 226_F | 1.284 | 0.99 |
| 266_R | 269_M | 1.275 | 0.99 |
| 439_T | 443_Y | 1.272 | 0.99 |
| 473_V | 477_F | 1.269 | 0.99 |
| 277_Y | 425_K | 1.267 | 0.99 |
| 349_V | 409_L | 1.265 | 0.99 |
| 101_L | 105_F | 1.261 | 0.99 |
| 82_L | 443_Y | 1.240 | 0.98 |
| 473_V | 476_F | 1.234 | 0.98 |
| 295_S | 479_Y | 1.233 | 0.98 |
| 136_G | 140_M | 1.225 | 0.98 |
| 100_L | 104_N | 1.216 | 0.98 |
| 196_D | 200_R | 1.211 | 0.98 |
| 178_V | 339_L | 1.207 | 0.98 |
| 174_C | 339_L | 1.206 | 0.98 |
| 360_A | 401_F | 1.204 | 0.98 |
| 235_E | 239_I | 1.201 | 0.98 |
| 448_A | 452_F | 1.199 | 0.98 |
| 112_I | 218_W | 1.195 | 0.98 |
| 337_L | 400_I | 1.191 | 0.98 |
| 119_I | 207_A | 1.190 | 0.98 |
| 161_H | 164_H | 1.189 | 0.98 |
| 459_K | 463_I | 1.187 | 0.98 |
| 372_W | 461_Y | 1.180 | 0.98 |
| 470_A | 474_F | 1.175 | 0.98 |
| 332_A | 336_G | 1.170 | 0.97 |
| 263_E | 266_R | 1.162 | 0.97 |
| 241_A | 254_V | 1.157 | 0.97 |
| 105_F | 113_I | 1.155 | 0.97 |
| 371_I | 394_F | 1.154 | 0.97 |
| 117_I | 144_G | 1.144 | 0.97 |
| 234_D | 237_L | 1.141 | 0.97 |
| 368_T | 397_V | 1.140 | 0.97 |
| 448_A | 460_L | 1.137 | 0.97 |
| 419_P | 422_L | 1.136 | 0.97 |
| 317_E | 327_K | 1.135 | 0.97 |
| 436_C | 440_L | 1.124 | 0.97 |
| 266_R | 270_E | 1.111 | 0.96 |
| 472_F | 476_F | 1.105 | 0.96 |
| 463_I | 467_W | 1.105 | 0.96 |
| 485_P | 490_L | 1.101 | 0.96 |
| 173_N | 408_G | 1.096 | 0.96 |
| 362_T | 471_E | 1.093 | 0.96 |
| 107_R | 222_E | 1.091 | 0.96 |
| 329_G | 333_G | 1.090 | 0.96 |
| 238_H | 241_A | 1.087 | 0.96 |
| 291_A | 295_S | 1.085 | 0.96 |
| 422_L | 426_G | 1.084 | 0.96 |
| 402_Y | 407_S | 1.084 | 0.96 |
| 228_I | 258_F | 1.083 | 0.96 |
| 360_A | 364_G | 1.081 | 0.95 |
| 85_A | 443_Y | 1.080 | 0.95 |
| 121_G | 141_L | 1.079 | 0.95 |
| 149_Q | 435_Q | 1.073 | 0.95 |
| 170_T | 412_G | 1.071 | 0.95 |
| 81_G | 447_V | 1.070 | 0.95 |
| 122_A | 207_A | 1.068 | 0.95 |
| 215_L | 219_W | 1.065 | 0.95 |
| 97_F | 143_F | 1.063 | 0.95 |
| 293_L | 426_G | 1.062 | 0.95 |
| 116_V | 120_V | 1.061 | 0.95 |
| 226_F | 232_K | 1.061 | 0.95 |
| 81_G | 446_P | 1.057 | 0.95 |
| 162_P | 486_T | 1.056 | 0.95 |
| 81_G | 85_A | 1.053 | 0.95 |
| 458_W | 462_L | 1.045 | 0.94 |
| 71_Y | 196_D | 1.042 | 0.94 |
| 85_A | 439_T | 1.040 | 0.94 |
| 286_N | 422_L | 1.040 | 0.94 |
| 363_G | 366_C | 1.039 | 0.94 |
| 342_S | 403_S | 1.038 | 0.94 |
| 291_A | 478_M | 1.035 | 0.94 |
| 154_M | 427_L | 1.028 | 0.94 |
| 118_M | 144_G | 1.027 | 0.94 |
| 177_N | 342_S | 1.026 | 0.94 |
| 83_L | 134_F | 1.023 | 0.93 |
| 411_V | 431_N | 1.023 | 0.93 |
| 156_L | 168_L | 1.021 | 0.93 |
| 94_S | 143_F | 1.020 | 0.93 |
| 196_D | 199_W | 1.017 | 0.93 |
| 347_L | 351_K | 1.012 | 0.93 |
| 240_L | 254_V | 1.012 | 0.93 |
| 106_G | 222_E | 1.006 | 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 | |
| 4ldsA | 2 | 0.8034 | 100 | 0.51 | Contact Map |
| 4pypA | 1 | 0.8187 | 100 | 0.513 | Contact Map |
| 4zw9A | 1 | 0 | 100 | 0.516 | Contact Map |
| 4gc0A | 1 | 0.8416 | 100 | 0.519 | Contact Map |
| 4j05A | 2 | 0.7462 | 100 | 0.533 | Contact Map |
| 1pw4A | 1 | 0.8073 | 100 | 0.628 | Contact Map |
| 3wdoA | 1 | 0.8168 | 100 | 0.633 | Contact Map |
| 3o7qA | 1 | 0.729 | 100 | 0.67 | Contact Map |
| 2gfpA | 2 | 0.7118 | 100 | 0.673 | Contact Map |
| 2cfqA | 1 | 0.7767 | 100 | 0.681 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)