| VgrG 1-520 |
| ID: | 1490184560 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 520 (487) | ||
| Sequences: | 2780 (1827.7) | ||
| Seq/Len: | 5.708 | ||
| Nf(neff/√len): | 82.8 |
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: 5.708).
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 |
| 416_Y | 473_I | 5.012 | 1.00 |
| 136_V | 179_L | 4.286 | 1.00 |
| 319_G | 369_L | 4.267 | 1.00 |
| 38_G | 48_Y | 4.217 | 1.00 |
| 118_D | 172_L | 3.934 | 1.00 |
| 130_K | 138_Q | 3.783 | 1.00 |
| 184_I | 201_F | 3.677 | 1.00 |
| 504_L | 517_L | 3.572 | 1.00 |
| 92_T | 111_K | 3.545 | 1.00 |
| 418_V | 436_V | 3.440 | 1.00 |
| 136_V | 175_I | 3.218 | 1.00 |
| 357_F | 365_L | 2.914 | 1.00 |
| 411_D | 415_M | 2.866 | 1.00 |
| 176_Q | 186_Y | 2.838 | 1.00 |
| 135_V | 164_I | 2.797 | 1.00 |
| 49_D | 107_R | 2.630 | 1.00 |
| 321_S | 367_V | 2.611 | 1.00 |
| 52_F | 108_I | 2.599 | 1.00 |
| 505_R | 514_H | 2.593 | 1.00 |
| 169_E | 177_R | 2.548 | 1.00 |
| 39_T | 356_L | 2.313 | 1.00 |
| 462_A | 474_A | 2.297 | 1.00 |
| 69_A | 110_L | 2.280 | 1.00 |
| 419_K | 426_D | 2.279 | 1.00 |
| 492_T | 507_E | 2.256 | 1.00 |
| 161_R | 182_V | 2.252 | 1.00 |
| 356_L | 368_M | 2.246 | 1.00 |
| 61_A | 94_F | 2.240 | 1.00 |
| 304_R | 308_E | 2.204 | 1.00 |
| 308_E | 381_R | 2.162 | 1.00 |
| 129_N | 162_E | 2.128 | 1.00 |
| 326_L | 352_L | 2.119 | 1.00 |
| 307_H | 311_L | 2.112 | 1.00 |
| 115_S | 118_D | 2.097 | 1.00 |
| 503_K | 516_K | 2.085 | 1.00 |
| 47_R | 109_T | 2.070 | 1.00 |
| 51_I | 107_R | 2.064 | 1.00 |
| 41_G | 44_K | 2.055 | 1.00 |
| 131_S | 134_E | 1.944 | 1.00 |
| 458_E | 479_D | 1.943 | 1.00 |
| 134_E | 137_E | 1.927 | 1.00 |
| 490_N | 493_R | 1.924 | 1.00 |
| 251_H | 413_S | 1.922 | 1.00 |
| 172_L | 176_Q | 1.922 | 1.00 |
| 460_A | 472_Y | 1.917 | 1.00 |
| 254_A | 480_S | 1.880 | 1.00 |
| 41_G | 354_Q | 1.874 | 1.00 |
| 457_T | 476_A | 1.872 | 1.00 |
| 45_I | 118_D | 1.866 | 1.00 |
| 134_E | 160_K | 1.864 | 1.00 |
| 124_H | 168_Q | 1.863 | 1.00 |
| 250_N | 253_E | 1.855 | 1.00 |
| 127_F | 142_E | 1.854 | 1.00 |
| 90_V | 116_L | 1.815 | 1.00 |
| 114_I | 172_L | 1.805 | 1.00 |
| 230_V | 369_L | 1.801 | 1.00 |
| 179_L | 201_F | 1.798 | 1.00 |
| 393_T | 462_A | 1.770 | 1.00 |
| 357_F | 367_V | 1.766 | 1.00 |
| 95_R | 107_R | 1.758 | 1.00 |
| 93_D | 238_R | 1.758 | 1.00 |
| 113_F | 140_L | 1.753 | 1.00 |
| 172_L | 186_Y | 1.748 | 1.00 |
| 441_P | 449_F | 1.743 | 1.00 |
| 139_I | 175_I | 1.730 | 1.00 |
| 451_F | 496_I | 1.724 | 1.00 |
| 509_K | 512_E | 1.722 | 1.00 |
| 94_F | 108_I | 1.699 | 1.00 |
| 161_R | 181_E | 1.696 | 1.00 |
| 140_L | 175_I | 1.692 | 1.00 |
| 354_Q | 370_S | 1.678 | 1.00 |
| 175_I | 179_L | 1.676 | 1.00 |
| 164_I | 182_V | 1.661 | 1.00 |
| 497_R | 503_K | 1.655 | 1.00 |
| 47_R | 111_K | 1.651 | 1.00 |
| 60_D | 63_W | 1.646 | 1.00 |
| 306_D | 309_R | 1.642 | 1.00 |
| 437_R | 458_E | 1.634 | 0.99 |
| 48_Y | 357_F | 1.620 | 0.99 |
| 233_L | 317_I | 1.606 | 0.99 |
| 40_E | 85_K | 1.597 | 0.99 |
| 460_A | 477_L | 1.573 | 0.99 |
| 417_R | 435_P | 1.543 | 0.99 |
| 45_I | 172_L | 1.528 | 0.99 |
| 505_R | 516_K | 1.528 | 0.99 |
| 352_L | 355_L | 1.523 | 0.99 |
| 48_Y | 110_L | 1.519 | 0.99 |
| 232_A | 320_K | 1.515 | 0.99 |
| 349_P | 374_Y | 1.511 | 0.99 |
| 133_P | 158_Y | 1.499 | 0.99 |
| 152_F | 201_F | 1.499 | 0.99 |
| 493_R | 505_R | 1.479 | 0.99 |
| 485_H | 488_D | 1.470 | 0.99 |
| 158_Y | 184_I | 1.469 | 0.99 |
| 333_T | 349_P | 1.464 | 0.99 |
| 493_R | 507_E | 1.462 | 0.99 |
| 420_F | 461_I | 1.461 | 0.99 |
| 486_V | 503_K | 1.459 | 0.99 |
| 249_Y | 397_R | 1.444 | 0.98 |
| 387_R | 467_D | 1.432 | 0.98 |
| 43_S | 382_P | 1.431 | 0.98 |
| 125_R | 142_E | 1.423 | 0.98 |
| 166_Q | 171_D | 1.423 | 0.98 |
| 277_E | 424_R | 1.422 | 0.98 |
| 400_S | 455_Q | 1.421 | 0.98 |
| 355_L | 367_V | 1.417 | 0.98 |
| 112_P | 188_F | 1.403 | 0.98 |
| 416_Y | 453_L | 1.402 | 0.98 |
| 111_K | 118_D | 1.401 | 0.98 |
| 399_T | 419_K | 1.398 | 0.98 |
| 139_I | 142_E | 1.393 | 0.98 |
| 111_K | 115_S | 1.392 | 0.98 |
| 88_H | 197_E | 1.391 | 0.98 |
| 36_F | 359_G | 1.387 | 0.98 |
| 185_F | 208_L | 1.377 | 0.98 |
| 320_K | 368_M | 1.370 | 0.98 |
| 328_P | 355_L | 1.370 | 0.98 |
| 436_V | 461_I | 1.368 | 0.98 |
| 117_L | 139_I | 1.361 | 0.98 |
| 401_A | 409_W | 1.357 | 0.97 |
| 176_Q | 180_A | 1.344 | 0.97 |
| 38_G | 87_V | 1.342 | 0.97 |
| 241_E | 278_V | 1.341 | 0.97 |
| 133_P | 154_L | 1.339 | 0.97 |
| 444_G | 457_T | 1.333 | 0.97 |
| 45_I | 112_P | 1.333 | 0.97 |
| 49_D | 109_T | 1.331 | 0.97 |
| 418_V | 461_I | 1.331 | 0.97 |
| 230_V | 321_S | 1.323 | 0.97 |
| 187_F | 202_G | 1.320 | 0.97 |
| 316_R | 370_S | 1.317 | 0.97 |
| 46_Y | 112_P | 1.317 | 0.97 |
| 447_Y | 457_T | 1.308 | 0.97 |
| 120_Q | 171_D | 1.307 | 0.97 |
| 492_T | 509_K | 1.304 | 0.97 |
| 126_F | 165_N | 1.299 | 0.96 |
| 42_I | 353_T | 1.292 | 0.96 |
| 37_S | 358_T | 1.289 | 0.96 |
| 35_D | 51_I | 1.288 | 0.96 |
| 50_I | 110_L | 1.280 | 0.96 |
| 127_F | 138_Q | 1.267 | 0.96 |
| 390_I | 462_A | 1.263 | 0.96 |
| 401_A | 455_Q | 1.254 | 0.95 |
| 497_R | 501_N | 1.253 | 0.95 |
| 488_D | 498_T | 1.244 | 0.95 |
| 37_S | 356_L | 1.244 | 0.95 |
| 123_T | 424_R | 1.243 | 0.95 |
| 161_R | 164_I | 1.239 | 0.95 |
| 137_E | 141_T | 1.236 | 0.95 |
| 395_T | 421_D | 1.228 | 0.95 |
| 402_K | 429_P | 1.227 | 0.95 |
| 68_S | 88_H | 1.227 | 0.95 |
| 93_D | 109_T | 1.226 | 0.95 |
| 461_I | 473_I | 1.220 | 0.94 |
| 418_V | 473_I | 1.220 | 0.94 |
| 158_Y | 203_D | 1.218 | 0.94 |
| 189_T | 200_H | 1.218 | 0.94 |
| 409_W | 435_P | 1.215 | 0.94 |
| 185_F | 202_G | 1.213 | 0.94 |
| 115_S | 119_K | 1.213 | 0.94 |
| 114_I | 199_I | 1.211 | 0.94 |
| 140_L | 201_F | 1.210 | 0.94 |
| 394_M | 465_E | 1.209 | 0.94 |
| 70_T | 88_H | 1.207 | 0.94 |
| 132_V | 182_V | 1.205 | 0.94 |
| 331_V | 349_P | 1.198 | 0.94 |
| 73_M | 87_V | 1.194 | 0.94 |
| 39_T | 354_Q | 1.191 | 0.93 |
| 463_F | 471_P | 1.190 | 0.93 |
| 309_R | 384_L | 1.182 | 0.93 |
| 48_Y | 87_V | 1.181 | 0.93 |
| 46_Y | 188_F | 1.178 | 0.93 |
| 233_L | 371_A | 1.173 | 0.93 |
| 501_N | 516_K | 1.171 | 0.93 |
| 300_N | 304_R | 1.164 | 0.92 |
| 202_G | 207_A | 1.162 | 0.92 |
| 214_L | 323_D | 1.157 | 0.92 |
| 168_Q | 280_H | 1.157 | 0.92 |
| 187_F | 200_H | 1.153 | 0.92 |
| 494_N | 498_T | 1.151 | 0.92 |
| 151_E | 189_T | 1.149 | 0.92 |
| 173_R | 176_Q | 1.149 | 0.92 |
| 88_H | 192_P | 1.148 | 0.92 |
| 120_Q | 170_S | 1.146 | 0.92 |
| 143_H | 171_D | 1.145 | 0.92 |
| 438_L | 473_I | 1.142 | 0.92 |
| 230_V | 334_I | 1.138 | 0.91 |
| 33_V | 71_L | 1.132 | 0.91 |
| 184_I | 382_P | 1.131 | 0.91 |
| 487_T | 498_T | 1.130 | 0.91 |
| 416_Y | 438_L | 1.129 | 0.91 |
| 319_G | 371_A | 1.124 | 0.91 |
| 137_E | 152_F | 1.123 | 0.91 |
| 132_V | 184_I | 1.121 | 0.90 |
| 500_A | 520_E | 1.104 | 0.90 |
| 168_Q | 465_E | 1.104 | 0.90 |
| 338_T | 347_Q | 1.101 | 0.89 |
| 69_A | 91_I | 1.101 | 0.89 |
| 439_A | 475_H | 1.100 | 0.89 |
| 331_V | 374_Y | 1.100 | 0.89 |
| 50_I | 71_L | 1.098 | 0.89 |
| 46_Y | 197_E | 1.093 | 0.89 |
| 490_N | 495_V | 1.092 | 0.89 |
| 320_K | 366_Q | 1.089 | 0.89 |
| 130_K | 134_E | 1.089 | 0.89 |
| 490_N | 498_T | 1.088 | 0.89 |
| 472_Y | 477_L | 1.086 | 0.89 |
| 54_S | 106_Y | 1.085 | 0.88 |
| 33_V | 50_I | 1.084 | 0.88 |
| 285_H | 299_A | 1.082 | 0.88 |
| 394_M | 463_F | 1.082 | 0.88 |
| 278_V | 310_F | 1.080 | 0.88 |
| 162_E | 251_H | 1.070 | 0.88 |
| 25_P | 67_K | 1.069 | 0.87 |
| 36_F | 71_L | 1.066 | 0.87 |
| 46_Y | 88_H | 1.066 | 0.87 |
| 189_T | 193_D | 1.064 | 0.87 |
| 34_E | 51_I | 1.062 | 0.87 |
| 233_L | 334_I | 1.058 | 0.87 |
| 420_F | 463_F | 1.056 | 0.87 |
| 132_V | 158_Y | 1.053 | 0.86 |
| 498_T | 515_I | 1.049 | 0.86 |
| 486_V | 516_K | 1.040 | 0.85 |
| 113_F | 145_L | 1.039 | 0.85 |
| 192_P | 197_E | 1.038 | 0.85 |
| 235_V | 315_T | 1.029 | 0.85 |
| 164_I | 174_F | 1.026 | 0.84 |
| 243_R | 277_E | 1.025 | 0.84 |
| 33_V | 36_F | 1.024 | 0.84 |
| 151_E | 198_V | 1.020 | 0.84 |
| 205_Q | 208_L | 1.017 | 0.84 |
| 180_A | 385_L | 1.010 | 0.83 |
| 46_Y | 192_P | 1.007 | 0.83 |
| 129_N | 160_K | 1.007 | 0.83 |
| 45_I | 186_Y | 1.005 | 0.83 |
| 210_F | 331_V | 1.002 | 0.82 |
| 506_M | 515_I | 1.001 | 0.82 |
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 | |
| 4mtkA | 6 | 0.9077 | 100 | 0.149 | Contact Map |
| 2p5zX | 1 | 0.6885 | 100 | 0.171 | Contact Map |
| 3d37A | 2 | 0.6 | 100 | 0.668 | Contact Map |
| 3cddA | 6 | 0.6058 | 100 | 0.681 | Contact Map |
| 1wruA | 1 | 0.6 | 100 | 0.682 | Contact Map |
| 3qr8A | 1 | 0.2269 | 99.9 | 0.807 | Contact Map |
| 1wthA | 1 | 0.5981 | 99.3 | 0.882 | Contact Map |
| 3pqiA | 1 | 0.2154 | 97.3 | 0.936 | Contact Map |
| 3gs9A | 1 | 0.5577 | 77.5 | 0.963 | Contact Map |
| 1wthD | 1 | 0.6231 | 22.2 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)