| bmp_gremlin |
| ID: | 1494388721 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 408 (359) | ||
| Sequences: | 557 (330.1) | ||
| Seq/Len: | 1.552 | ||
| Nf(neff/√len): | 17.4 |
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: 1.552).
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 |
| 314_Y | 331_G | 3.481 | 1.00 |
| 83_M | 86_L | 2.767 | 1.00 |
| 224_W | 231_N | 2.762 | 1.00 |
| 322_W | 325_W | 2.448 | 1.00 |
| 224_W | 233_G | 2.255 | 0.99 |
| 381_I | 401_V | 2.033 | 0.98 |
| 83_M | 119_S | 1.936 | 0.98 |
| 161_F | 212_W | 1.905 | 0.97 |
| 67_L | 71_P | 1.780 | 0.95 |
| 62_L | 71_P | 1.777 | 0.95 |
| 327_V | 391_K | 1.725 | 0.94 |
| 387_D | 391_K | 1.632 | 0.92 |
| 182_E | 223_R | 1.608 | 0.91 |
| 356_I | 360_L | 1.583 | 0.90 |
| 379_S | 403_E | 1.573 | 0.90 |
| 357_V | 397_Y | 1.567 | 0.90 |
| 310_R | 335_F | 1.554 | 0.89 |
| 181_Y | 372_C | 1.509 | 0.87 |
| 217_V | 234_L | 1.490 | 0.86 |
| 352_T | 355_A | 1.475 | 0.86 |
| 384_L | 387_D | 1.471 | 0.85 |
| 354_H | 358_Q | 1.464 | 0.85 |
| 181_Y | 332_Y | 1.461 | 0.85 |
| 285_T | 288_R | 1.454 | 0.84 |
| 332_Y | 400_M | 1.453 | 0.84 |
| 344_P | 354_H | 1.445 | 0.84 |
| 379_S | 387_D | 1.438 | 0.84 |
| 328_A | 332_Y | 1.437 | 0.84 |
| 160_L | 180_I | 1.433 | 0.83 |
| 253_R | 256_R | 1.426 | 0.83 |
| 332_Y | 361_V | 1.418 | 0.82 |
| 78_V | 178_I | 1.397 | 0.81 |
| 353_N | 358_Q | 1.388 | 0.81 |
| 355_A | 358_Q | 1.386 | 0.80 |
| 115_N | 118_R | 1.381 | 0.80 |
| 186_P | 198_R | 1.378 | 0.80 |
| 343_F | 359_T | 1.375 | 0.80 |
| 326_I | 385_Y | 1.368 | 0.79 |
| 141_L | 231_N | 1.360 | 0.79 |
| 212_W | 270_P | 1.355 | 0.78 |
| 352_T | 356_I | 1.350 | 0.78 |
| 326_I | 388_E | 1.347 | 0.78 |
| 228_K | 231_N | 1.338 | 0.77 |
| 140_F | 162_R | 1.337 | 0.77 |
| 65_F | 71_P | 1.325 | 0.76 |
| 381_I | 397_Y | 1.325 | 0.76 |
| 61_L | 65_F | 1.317 | 0.75 |
| 358_Q | 369_P | 1.315 | 0.75 |
| 308_C | 337_C | 1.315 | 0.75 |
| 308_C | 339_G | 1.315 | 0.75 |
| 118_R | 151_E | 1.298 | 0.74 |
| 143_N | 374_V | 1.297 | 0.74 |
| 142_F | 158_L | 1.289 | 0.73 |
| 355_A | 394_L | 1.284 | 0.73 |
| 272_L | 323_N | 1.283 | 0.73 |
| 388_E | 391_K | 1.283 | 0.73 |
| 201_D | 216_D | 1.283 | 0.73 |
| 331_G | 392_V | 1.280 | 0.72 |
| 224_W | 394_L | 1.275 | 0.72 |
| 313_L | 322_W | 1.274 | 0.72 |
| 328_A | 359_T | 1.271 | 0.72 |
| 344_P | 358_Q | 1.266 | 0.71 |
| 321_G | 387_D | 1.256 | 0.70 |
| 343_F | 356_I | 1.253 | 0.70 |
| 308_C | 317_F | 1.251 | 0.70 |
| 82_Y | 273_V | 1.251 | 0.70 |
| 313_L | 361_V | 1.244 | 0.69 |
| 61_L | 272_L | 1.244 | 0.69 |
| 313_L | 334_A | 1.236 | 0.69 |
| 379_S | 402_V | 1.229 | 0.68 |
| 344_P | 353_N | 1.226 | 0.68 |
| 57_F | 61_L | 1.224 | 0.68 |
| 317_F | 334_A | 1.223 | 0.67 |
| 316_D | 390_D | 1.222 | 0.67 |
| 374_V | 408_R | 1.221 | 0.67 |
| 285_T | 289_R | 1.212 | 0.66 |
| 350_N | 369_P | 1.205 | 0.66 |
| 323_N | 388_E | 1.204 | 0.66 |
| 344_P | 355_A | 1.204 | 0.66 |
| 231_N | 234_L | 1.195 | 0.65 |
| 49_Q | 53_L | 1.192 | 0.65 |
| 61_L | 115_N | 1.191 | 0.64 |
| 314_Y | 319_D | 1.187 | 0.64 |
| 400_M | 405_C | 1.181 | 0.64 |
| 82_Y | 161_F | 1.179 | 0.63 |
| 217_V | 272_L | 1.173 | 0.63 |
| 50_S | 54_L | 1.164 | 0.62 |
| 70_R | 324_D | 1.162 | 0.62 |
| 402_V | 405_C | 1.162 | 0.62 |
| 338_H | 347_D | 1.162 | 0.62 |
| 344_P | 352_T | 1.162 | 0.62 |
| 320_V | 369_P | 1.161 | 0.62 |
| 317_F | 354_H | 1.159 | 0.61 |
| 215_F | 234_L | 1.155 | 0.61 |
| 87_Y | 157_E | 1.151 | 0.61 |
| 384_L | 394_L | 1.147 | 0.60 |
| 340_D | 370_K | 1.146 | 0.60 |
| 316_D | 383_M | 1.146 | 0.60 |
| 228_K | 233_G | 1.144 | 0.60 |
| 314_Y | 344_P | 1.143 | 0.60 |
| 340_D | 393_V | 1.141 | 0.60 |
| 386_L | 396_N | 1.137 | 0.59 |
| 354_H | 394_L | 1.135 | 0.59 |
| 363_S | 403_E | 1.132 | 0.59 |
| 355_A | 378_L | 1.131 | 0.59 |
| 115_N | 119_S | 1.131 | 0.59 |
| 298_S | 301_A | 1.130 | 0.58 |
| 404_G | 408_R | 1.129 | 0.58 |
| 379_S | 382_S | 1.127 | 0.58 |
| 82_Y | 85_D | 1.125 | 0.58 |
| 355_A | 369_P | 1.123 | 0.58 |
| 122_H | 270_P | 1.120 | 0.57 |
| 224_W | 356_I | 1.118 | 0.57 |
| 350_N | 356_I | 1.112 | 0.57 |
| 147_I | 274_T | 1.109 | 0.56 |
| 313_L | 402_V | 1.107 | 0.56 |
| 322_W | 400_M | 1.104 | 0.56 |
| 357_V | 395_K | 1.101 | 0.55 |
| 83_M | 140_F | 1.101 | 0.55 |
| 353_N | 356_I | 1.099 | 0.55 |
| 319_D | 402_V | 1.099 | 0.55 |
| 66_G | 392_V | 1.098 | 0.55 |
| 116_T | 216_D | 1.096 | 0.55 |
| 331_G | 350_N | 1.095 | 0.55 |
| 153_I | 315_V | 1.089 | 0.54 |
| 378_L | 385_Y | 1.089 | 0.54 |
| 120_F | 326_I | 1.087 | 0.54 |
| 328_A | 369_P | 1.083 | 0.54 |
| 321_G | 332_Y | 1.082 | 0.54 |
| 116_T | 393_V | 1.082 | 0.54 |
| 60_T | 64_M | 1.081 | 0.53 |
| 72_Q | 84_R | 1.080 | 0.53 |
| 159_R | 212_W | 1.079 | 0.53 |
| 323_N | 327_V | 1.079 | 0.53 |
| 402_V | 407_C | 1.079 | 0.53 |
| 359_T | 363_S | 1.075 | 0.53 |
| 351_S | 355_A | 1.071 | 0.52 |
| 65_F | 197_T | 1.071 | 0.52 |
| 313_L | 319_D | 1.070 | 0.52 |
| 344_P | 356_I | 1.068 | 0.52 |
| 350_N | 353_N | 1.063 | 0.52 |
| 213_E | 326_I | 1.061 | 0.51 |
| 276_G | 383_M | 1.058 | 0.51 |
| 319_D | 336_Y | 1.057 | 0.51 |
| 140_F | 202_T | 1.055 | 0.51 |
| 356_I | 408_R | 1.055 | 0.51 |
| 219_P | 382_S | 1.054 | 0.51 |
| 178_I | 289_R | 1.053 | 0.51 |
| 330_P | 391_K | 1.052 | 0.50 |
| 50_S | 53_L | 1.051 | 0.50 |
| 233_G | 313_L | 1.048 | 0.50 |
| 317_F | 337_C | 1.048 | 0.50 |
| 317_F | 339_G | 1.048 | 0.50 |
| 387_D | 392_V | 1.046 | 0.50 |
| 322_W | 357_V | 1.041 | 0.49 |
| 402_V | 406_G | 1.041 | 0.49 |
| 80_P | 331_G | 1.040 | 0.49 |
| 340_D | 383_M | 1.039 | 0.49 |
| 332_Y | 357_V | 1.037 | 0.49 |
| 324_D | 346_A | 1.037 | 0.49 |
| 61_L | 277_H | 1.037 | 0.49 |
| 156_A | 385_Y | 1.036 | 0.49 |
| 328_A | 350_N | 1.034 | 0.49 |
| 354_H | 371_A | 1.034 | 0.49 |
| 80_P | 394_L | 1.032 | 0.48 |
| 62_L | 325_W | 1.032 | 0.48 |
| 328_A | 384_L | 1.031 | 0.48 |
| 216_D | 362_N | 1.030 | 0.48 |
| 354_H | 372_C | 1.029 | 0.48 |
| 378_L | 401_V | 1.026 | 0.48 |
| 251_H | 271_L | 1.021 | 0.47 |
| 344_P | 406_G | 1.019 | 0.47 |
| 181_Y | 232_Y | 1.018 | 0.47 |
| 156_A | 184_M | 1.017 | 0.47 |
| 400_M | 407_C | 1.017 | 0.47 |
| 145_S | 269_R | 1.015 | 0.47 |
| 66_G | 340_D | 1.015 | 0.47 |
| 343_F | 360_L | 1.014 | 0.46 |
| 192_P | 336_Y | 1.013 | 0.46 |
| 344_P | 393_V | 1.010 | 0.46 |
| 310_R | 333_Q | 1.009 | 0.46 |
| 142_F | 156_A | 1.007 | 0.46 |
| 355_A | 406_G | 1.007 | 0.46 |
| 118_R | 408_R | 1.006 | 0.46 |
| 118_R | 271_L | 1.006 | 0.46 |
| 328_A | 355_A | 1.005 | 0.46 |
| 83_M | 389_Y | 1.002 | 0.45 |
| 381_I | 394_L | 1.001 | 0.45 |
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 | |
| 3rjrA | 4 | 0.8064 | 100 | 0.36 | Contact Map |
| 2h62A | 2 | 0.2549 | 100 | 0.608 | Contact Map |
| 1lxiA | 1 | 0.2525 | 100 | 0.61 | Contact Map |
| 2r52A | 2 | 0.2549 | 100 | 0.611 | Contact Map |
| 4n1dA | 1 | 0.2549 | 100 | 0.612 | Contact Map |
| 3evsB | 1 | 0.2525 | 100 | 0.614 | Contact Map |
| 4mplA | 1 | 0.2574 | 100 | 0.622 | Contact Map |
| 2qcqA | 2 | 0.2598 | 100 | 0.624 | Contact Map |
| 2arpA | 1 | 0.25 | 100 | 0.639 | Contact Map |
| 2tgiA | 1 | 0.2696 | 100 | 0.66 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)