| 1BVYA |
| ID: | 1495651503 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 458 (449) | ||
| Sequences: | 25322 (17463.4) | ||
| Seq/Len: | 56.396 | ||
| Nf(neff/√len): | 824.1 |
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: 56.396).
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 |
| 316_M | 380_E | 4.717 | 1.00 |
| 370_D | 373_E | 3.947 | 1.00 |
| 370_D | 375_R | 3.679 | 1.00 |
| 292_E | 296_R | 3.391 | 1.00 |
| 276_A | 414_L | 3.390 | 1.00 |
| 288_Q | 292_E | 3.385 | 1.00 |
| 279_F | 325_W | 3.352 | 1.00 |
| 286_V | 313_Y | 3.340 | 1.00 |
| 289_K | 377_E | 3.177 | 1.00 |
| 422_D | 449_K | 3.118 | 1.00 |
| 224_K | 251_D | 2.985 | 1.00 |
| 315_G | 411_T | 2.882 | 1.00 |
| 276_A | 321_A | 2.853 | 1.00 |
| 362_R | 372_E | 2.850 | 1.00 |
| 223_R | 232_D | 2.803 | 1.00 |
| 290_A | 317_V | 2.769 | 1.00 |
| 368_G | 371_V | 2.754 | 1.00 |
| 148_L | 413_V | 2.737 | 1.00 |
| 348_E | 351_D | 2.696 | 1.00 |
| 272_L | 410_A | 2.600 | 1.00 |
| 145_M | 277_L | 2.557 | 1.00 |
| 338_D | 349_K | 2.503 | 1.00 |
| 291_A | 451_K | 2.498 | 1.00 |
| 290_A | 418_L | 2.491 | 1.00 |
| 291_A | 422_D | 2.477 | 1.00 |
| 30_M | 34_D | 2.414 | 1.00 |
| 221_A | 225_A | 2.401 | 1.00 |
| 276_A | 317_V | 2.333 | 1.00 |
| 289_K | 313_Y | 2.322 | 1.00 |
| 291_A | 295_A | 2.322 | 1.00 |
| 217_D | 221_A | 2.309 | 1.00 |
| 131_E | 420_H | 2.301 | 1.00 |
| 221_A | 251_D | 2.295 | 1.00 |
| 288_Q | 422_D | 2.270 | 1.00 |
| 39_I | 52_L | 2.243 | 1.00 |
| 295_A | 451_K | 2.230 | 1.00 |
| 364_K | 371_V | 2.209 | 1.00 |
| 290_A | 314_V | 2.195 | 1.00 |
| 287_L | 422_D | 2.124 | 1.00 |
| 131_E | 450_S | 2.110 | 1.00 |
| 145_M | 273_L | 2.103 | 1.00 |
| 338_D | 346_P | 2.085 | 1.00 |
| 131_E | 421_F | 2.083 | 1.00 |
| 318_L | 410_A | 2.054 | 1.00 |
| 217_D | 255_R | 2.034 | 1.00 |
| 417_M | 423_F | 2.021 | 1.00 |
| 287_L | 291_A | 2.014 | 1.00 |
| 124_V | 416_M | 2.004 | 1.00 |
| 288_Q | 291_A | 1.996 | 1.00 |
| 340_V | 346_P | 1.993 | 1.00 |
| 364_K | 369_D | 1.982 | 1.00 |
| 121_D | 155_L | 1.940 | 1.00 |
| 324_L | 362_R | 1.923 | 1.00 |
| 217_D | 251_D | 1.917 | 1.00 |
| 276_A | 280_L | 1.910 | 1.00 |
| 214_D | 218_K | 1.868 | 1.00 |
| 279_F | 283_N | 1.858 | 1.00 |
| 280_L | 286_V | 1.857 | 1.00 |
| 273_L | 413_V | 1.855 | 1.00 |
| 281_V | 287_L | 1.853 | 1.00 |
| 358_P | 362_R | 1.843 | 1.00 |
| 16_N | 19_L | 1.840 | 1.00 |
| 317_V | 374_F | 1.831 | 1.00 |
| 28_A | 31_K | 1.824 | 1.00 |
| 304_S | 307_Q | 1.810 | 1.00 |
| 52_L | 61_A | 1.789 | 1.00 |
| 210_K | 214_D | 1.768 | 1.00 |
| 67_F | 339_T | 1.762 | 1.00 |
| 313_Y | 377_E | 1.752 | 1.00 |
| 335_A | 347_L | 1.743 | 1.00 |
| 423_F | 448_A | 1.737 | 1.00 |
| 277_L | 417_M | 1.729 | 1.00 |
| 283_N | 286_V | 1.726 | 1.00 |
| 364_K | 372_E | 1.726 | 1.00 |
| 294_A | 415_G | 1.719 | 1.00 |
| 58_I | 360_L | 1.712 | 1.00 |
| 286_V | 317_V | 1.711 | 1.00 |
| 99_A | 257_Q | 1.709 | 1.00 |
| 11_F | 14_L | 1.701 | 1.00 |
| 272_L | 327_T | 1.683 | 1.00 |
| 279_F | 324_L | 1.673 | 1.00 |
| 293_E | 311_L | 1.672 | 1.00 |
| 123_A | 148_L | 1.672 | 1.00 |
| 218_K | 222_D | 1.653 | 1.00 |
| 31_K | 35_E | 1.634 | 1.00 |
| 31_K | 34_D | 1.630 | 1.00 |
| 12_G | 15_K | 1.624 | 1.00 |
| 250_D | 253_N | 1.624 | 1.00 |
| 337_E | 349_K | 1.597 | 1.00 |
| 125_Q | 166_Y | 1.584 | 1.00 |
| 399_A | 403_Q | 1.572 | 1.00 |
| 30_M | 359_Q | 1.558 | 1.00 |
| 297_V | 311_L | 1.550 | 1.00 |
| 14_L | 18_P | 1.548 | 1.00 |
| 294_A | 311_L | 1.545 | 1.00 |
| 320_E | 323_R | 1.542 | 1.00 |
| 7_Q | 36_L | 1.534 | 1.00 |
| 316_M | 377_E | 1.500 | 1.00 |
| 295_A | 419_K | 1.494 | 1.00 |
| 66_R | 337_E | 1.484 | 1.00 |
| 406_A | 410_A | 1.481 | 1.00 |
| 120_V | 416_M | 1.443 | 1.00 |
| 361_H | 392_P | 1.439 | 1.00 |
| 315_G | 319_N | 1.438 | 1.00 |
| 148_L | 152_T | 1.433 | 1.00 |
| 280_L | 287_L | 1.430 | 1.00 |
| 160_Y | 222_D | 1.419 | 1.00 |
| 277_L | 446_V | 1.418 | 1.00 |
| 140_E | 143_E | 1.415 | 1.00 |
| 41_K | 48_V | 1.414 | 1.00 |
| 221_A | 224_K | 1.410 | 1.00 |
| 235_T | 239_N | 1.408 | 1.00 |
| 7_Q | 16_N | 1.390 | 0.99 |
| 38_E | 54_S | 1.383 | 0.99 |
| 153_I | 265_G | 1.381 | 0.99 |
| 222_D | 226_S | 1.363 | 0.99 |
| 338_D | 348_E | 1.362 | 0.99 |
| 122_I | 125_Q | 1.360 | 0.99 |
| 154_G | 162_F | 1.357 | 0.99 |
| 94_K | 97_K | 1.355 | 0.99 |
| 112_M | 408_H | 1.351 | 0.99 |
| 334_Y | 350_G | 1.350 | 0.99 |
| 40_F | 51_Y | 1.336 | 0.99 |
| 54_S | 57_L | 1.329 | 0.99 |
| 278_Y | 282_K | 1.329 | 0.99 |
| 375_R | 381_N | 1.327 | 0.99 |
| 317_V | 321_A | 1.327 | 0.99 |
| 94_K | 98_K | 1.326 | 0.99 |
| 175_T | 179_R | 1.317 | 0.99 |
| 279_F | 321_A | 1.317 | 0.99 |
| 98_K | 253_N | 1.316 | 0.99 |
| 130_W | 144_D | 1.315 | 0.99 |
| 319_N | 407_L | 1.312 | 0.99 |
| 96_W | 100_H | 1.309 | 0.99 |
| 319_N | 390_F | 1.306 | 0.99 |
| 122_I | 155_L | 1.292 | 0.99 |
| 150_L | 266_H | 1.287 | 0.99 |
| 294_A | 314_V | 1.283 | 0.99 |
| 361_H | 390_F | 1.268 | 0.99 |
| 340_V | 344_E | 1.264 | 0.99 |
| 289_K | 292_E | 1.263 | 0.99 |
| 141_V | 277_L | 1.262 | 0.99 |
| 156_C | 405_F | 1.255 | 0.99 |
| 219_I | 222_D | 1.255 | 0.99 |
| 86_L | 401_I | 1.254 | 0.99 |
| 129_K | 144_D | 1.248 | 0.99 |
| 291_A | 418_L | 1.241 | 0.98 |
| 153_I | 157_G | 1.239 | 0.98 |
| 273_L | 410_A | 1.231 | 0.98 |
| 322_L | 392_P | 1.230 | 0.98 |
| 5_M | 50_R | 1.229 | 0.98 |
| 52_L | 57_L | 1.228 | 0.98 |
| 321_A | 374_F | 1.214 | 0.98 |
| 276_A | 318_L | 1.212 | 0.98 |
| 163_N | 166_Y | 1.209 | 0.98 |
| 172_P | 211_V | 1.205 | 0.98 |
| 85_G | 260_T | 1.199 | 0.98 |
| 280_L | 290_A | 1.198 | 0.98 |
| 407_L | 411_T | 1.197 | 0.98 |
| 28_A | 32_I | 1.193 | 0.98 |
| 222_D | 225_A | 1.187 | 0.98 |
| 213_N | 255_R | 1.181 | 0.98 |
| 34_D | 364_K | 1.180 | 0.98 |
| 84_D | 95_N | 1.169 | 0.97 |
| 213_N | 252_E | 1.168 | 0.97 |
| 128_Q | 131_E | 1.164 | 0.97 |
| 43_E | 48_V | 1.163 | 0.97 |
| 155_L | 161_R | 1.155 | 0.97 |
| 11_F | 18_P | 1.151 | 0.97 |
| 129_K | 132_R | 1.144 | 0.97 |
| 277_L | 414_L | 1.143 | 0.97 |
| 285_H | 289_K | 1.138 | 0.97 |
| 281_V | 446_V | 1.136 | 0.97 |
| 301_P | 307_Q | 1.135 | 0.97 |
| 298_L | 419_K | 1.133 | 0.97 |
| 346_P | 349_K | 1.128 | 0.97 |
| 279_F | 282_K | 1.125 | 0.97 |
| 272_L | 321_A | 1.125 | 0.97 |
| 286_V | 377_E | 1.123 | 0.97 |
| 53_S | 363_D | 1.117 | 0.96 |
| 127_V | 421_F | 1.110 | 0.96 |
| 120_V | 124_V | 1.107 | 0.96 |
| 32_I | 40_F | 1.103 | 0.96 |
| 149_T | 269_T | 1.103 | 0.96 |
| 277_L | 418_L | 1.101 | 0.96 |
| 322_L | 390_F | 1.099 | 0.96 |
| 103_L | 401_I | 1.099 | 0.96 |
| 95_N | 98_K | 1.098 | 0.96 |
| 50_R | 351_D | 1.095 | 0.96 |
| 89_S | 95_N | 1.090 | 0.96 |
| 95_N | 253_N | 1.090 | 0.96 |
| 416_M | 420_H | 1.086 | 0.96 |
| 58_I | 355_V | 1.085 | 0.96 |
| 357_I | 391_K | 1.084 | 0.96 |
| 203_R | 207_E | 1.080 | 0.95 |
| 213_N | 217_D | 1.078 | 0.95 |
| 122_I | 161_R | 1.074 | 0.95 |
| 56_R | 59_K | 1.072 | 0.95 |
| 126_L | 148_L | 1.062 | 0.95 |
| 249_L | 253_N | 1.062 | 0.95 |
| 232_D | 235_T | 1.061 | 0.95 |
| 281_V | 423_F | 1.058 | 0.95 |
| 123_A | 127_V | 1.057 | 0.95 |
| 176_S | 211_V | 1.047 | 0.94 |
| 10_T | 16_N | 1.044 | 0.94 |
| 334_Y | 352_E | 1.042 | 0.94 |
| 127_V | 416_M | 1.041 | 0.94 |
| 52_L | 58_I | 1.039 | 0.94 |
| 312_K | 316_M | 1.039 | 0.94 |
| 38_E | 365_T | 1.038 | 0.94 |
| 224_K | 241_K | 1.038 | 0.94 |
| 286_V | 375_R | 1.035 | 0.94 |
| 416_M | 419_K | 1.031 | 0.94 |
| 107_F | 401_I | 1.030 | 0.94 |
| 143_E | 147_R | 1.027 | 0.94 |
| 59_K | 63_D | 1.026 | 0.94 |
| 60_E | 342_G | 1.026 | 0.94 |
| 123_A | 412_L | 1.026 | 0.94 |
| 50_R | 347_L | 1.024 | 0.93 |
| 307_Q | 310_Q | 1.018 | 0.93 |
| 403_Q | 407_L | 1.015 | 0.93 |
| 223_R | 235_T | 1.013 | 0.93 |
| 124_V | 128_Q | 1.013 | 0.93 |
| 285_H | 288_Q | 1.007 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2ij2A | 2 | 0.9913 | 100 | 0.082 | Contact Map |
| 4r21A | 2 | 0.893 | 100 | 0.152 | Contact Map |
| 3k9vA | 2 | 0.9629 | 100 | 0.155 | Contact Map |
| 3czhA | 2 | 0.9716 | 100 | 0.156 | Contact Map |
| 3dbgA | 2 | 0.8231 | 100 | 0.159 | Contact Map |
| 3tbgA | 4 | 0.9672 | 100 | 0.16 | Contact Map |
| 2ve3A | 2 | 0.9323 | 100 | 0.163 | Contact Map |
| 3nxuA | 2 | 0.9454 | 100 | 0.163 | Contact Map |
| 3pm0A | 1 | 0.9301 | 100 | 0.167 | Contact Map |
| 2hi4A | 1 | 0.9738 | 100 | 0.169 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)