| Pgl |
| ID: | 1488469909 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 476 (460) | ||
| Sequences: | 1421 (919.6) | ||
| Seq/Len: | 3.089 | ||
| Nf(neff/√len): | 42.9 |
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: 3.089).
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 |
| 441_N | 445_A | 2.785 | 1.00 |
| 456_F | 459_L | 2.610 | 1.00 |
| 441_N | 446_R | 2.519 | 1.00 |
| 446_R | 468_T | 2.467 | 1.00 |
| 120_A | 124_A | 2.423 | 1.00 |
| 455_A | 459_L | 2.330 | 1.00 |
| 455_A | 458_L | 2.254 | 1.00 |
| 435_L | 439_L | 2.192 | 1.00 |
| 155_S | 190_T | 2.088 | 1.00 |
| 86_E | 89_R | 2.051 | 1.00 |
| 35_Y | 39_E | 2.047 | 1.00 |
| 107_V | 112_R | 1.943 | 1.00 |
| 40_N | 44_N | 1.901 | 0.99 |
| 108_Y | 158_G | 1.884 | 0.99 |
| 110_L | 119_A | 1.870 | 0.99 |
| 110_L | 120_A | 1.859 | 0.99 |
| 455_A | 460_I | 1.851 | 0.99 |
| 457_A | 460_I | 1.850 | 0.99 |
| 340_T | 383_L | 1.809 | 0.99 |
| 459_L | 473_D | 1.801 | 0.99 |
| 454_V | 458_L | 1.733 | 0.99 |
| 36_R | 52_D | 1.731 | 0.99 |
| 447_N | 450_S | 1.730 | 0.99 |
| 460_I | 470_I | 1.703 | 0.98 |
| 460_I | 473_D | 1.694 | 0.98 |
| 112_R | 117_K | 1.681 | 0.98 |
| 439_L | 461_A | 1.615 | 0.98 |
| 442_A | 446_R | 1.608 | 0.98 |
| 459_L | 468_T | 1.597 | 0.97 |
| 158_G | 162_L | 1.592 | 0.97 |
| 463_A | 470_I | 1.585 | 0.97 |
| 437_R | 441_N | 1.581 | 0.97 |
| 331_V | 334_P | 1.577 | 0.97 |
| 12_I | 15_P | 1.573 | 0.97 |
| 470_I | 473_D | 1.568 | 0.97 |
| 433_L | 436_Y | 1.562 | 0.97 |
| 460_I | 471_L | 1.554 | 0.97 |
| 458_L | 462_L | 1.549 | 0.97 |
| 454_V | 457_A | 1.546 | 0.97 |
| 107_V | 117_K | 1.541 | 0.97 |
| 454_V | 462_L | 1.520 | 0.96 |
| 101_V | 105_L | 1.515 | 0.96 |
| 212_M | 216_F | 1.502 | 0.96 |
| 76_A | 143_N | 1.495 | 0.96 |
| 159_T | 183_Y | 1.492 | 0.96 |
| 328_V | 331_V | 1.488 | 0.96 |
| 269_G | 272_V | 1.461 | 0.95 |
| 456_F | 460_I | 1.455 | 0.95 |
| 14_N | 18_S | 1.446 | 0.95 |
| 79_I | 83_T | 1.442 | 0.95 |
| 146_H | 149_E | 1.427 | 0.94 |
| 455_A | 461_A | 1.427 | 0.94 |
| 105_L | 155_S | 1.425 | 0.94 |
| 101_V | 151_F | 1.421 | 0.94 |
| 449_L | 468_T | 1.412 | 0.94 |
| 328_V | 332_V | 1.407 | 0.94 |
| 453_R | 462_L | 1.406 | 0.94 |
| 434_H | 439_L | 1.403 | 0.93 |
| 32_W | 464_A | 1.401 | 0.93 |
| 456_F | 473_D | 1.391 | 0.93 |
| 13_L | 17_N | 1.377 | 0.93 |
| 15_P | 18_S | 1.377 | 0.93 |
| 163_A | 187_A | 1.376 | 0.93 |
| 434_H | 441_N | 1.375 | 0.93 |
| 452_F | 468_T | 1.374 | 0.93 |
| 320_D | 327_S | 1.371 | 0.92 |
| 457_A | 461_A | 1.370 | 0.92 |
| 458_L | 461_A | 1.364 | 0.92 |
| 460_I | 474_A | 1.363 | 0.92 |
| 194_Y | 201_G | 1.357 | 0.92 |
| 313_L | 317_I | 1.355 | 0.92 |
| 436_Y | 439_L | 1.349 | 0.92 |
| 435_L | 441_N | 1.344 | 0.91 |
| 222_V | 226_R | 1.340 | 0.91 |
| 206_P | 233_A | 1.339 | 0.91 |
| 445_A | 454_V | 1.338 | 0.91 |
| 460_I | 463_A | 1.338 | 0.91 |
| 208_I | 378_S | 1.334 | 0.91 |
| 35_Y | 38_I | 1.322 | 0.91 |
| 439_L | 442_A | 1.321 | 0.90 |
| 456_F | 468_T | 1.318 | 0.90 |
| 101_V | 104_I | 1.316 | 0.90 |
| 56_Y | 62_Y | 1.315 | 0.90 |
| 340_T | 352_N | 1.313 | 0.90 |
| 443_I | 446_R | 1.296 | 0.89 |
| 435_L | 461_A | 1.296 | 0.89 |
| 77_G | 81_S | 1.292 | 0.89 |
| 33_Y | 36_R | 1.291 | 0.89 |
| 455_A | 473_D | 1.287 | 0.89 |
| 460_I | 475_Q | 1.285 | 0.89 |
| 444_G | 452_F | 1.279 | 0.89 |
| 442_A | 468_T | 1.279 | 0.89 |
| 119_A | 403_A | 1.270 | 0.88 |
| 5_L | 12_I | 1.270 | 0.88 |
| 275_A | 278_Y | 1.263 | 0.88 |
| 450_S | 473_D | 1.263 | 0.88 |
| 259_Y | 263_Q | 1.262 | 0.88 |
| 463_A | 469_Y | 1.257 | 0.87 |
| 457_A | 473_D | 1.256 | 0.87 |
| 408_N | 412_Y | 1.252 | 0.87 |
| 331_V | 388_F | 1.252 | 0.87 |
| 442_A | 462_L | 1.233 | 0.86 |
| 309_L | 315_F | 1.231 | 0.86 |
| 459_L | 466_Y | 1.229 | 0.86 |
| 97_A | 189_I | 1.228 | 0.86 |
| 437_R | 440_E | 1.227 | 0.86 |
| 159_T | 186_I | 1.227 | 0.86 |
| 9_K | 16_W | 1.223 | 0.85 |
| 363_H | 366_A | 1.222 | 0.85 |
| 30_D | 58_P | 1.216 | 0.85 |
| 11_R | 15_P | 1.212 | 0.85 |
| 8_V | 14_N | 1.209 | 0.84 |
| 161_L | 165_N | 1.207 | 0.84 |
| 445_A | 449_L | 1.194 | 0.83 |
| 113_E | 162_L | 1.185 | 0.83 |
| 307_T | 314_F | 1.183 | 0.83 |
| 449_L | 459_L | 1.180 | 0.82 |
| 7_S | 10_L | 1.179 | 0.82 |
| 456_F | 461_A | 1.178 | 0.82 |
| 3_A | 6_I | 1.175 | 0.82 |
| 112_R | 116_D | 1.171 | 0.82 |
| 431_D | 435_L | 1.160 | 0.81 |
| 449_L | 460_I | 1.153 | 0.80 |
| 54_F | 206_P | 1.152 | 0.80 |
| 7_S | 12_I | 1.150 | 0.80 |
| 439_L | 455_A | 1.148 | 0.80 |
| 159_T | 209_L | 1.146 | 0.80 |
| 160_F | 212_M | 1.146 | 0.80 |
| 13_L | 16_W | 1.137 | 0.79 |
| 464_A | 470_I | 1.135 | 0.79 |
| 95_I | 99_G | 1.134 | 0.79 |
| 445_A | 468_T | 1.133 | 0.79 |
| 435_L | 458_L | 1.132 | 0.79 |
| 467_P | 472_A | 1.129 | 0.78 |
| 447_N | 468_T | 1.129 | 0.78 |
| 12_I | 16_W | 1.125 | 0.78 |
| 438_A | 441_N | 1.122 | 0.78 |
| 463_A | 468_T | 1.122 | 0.78 |
| 140_L | 143_N | 1.119 | 0.78 |
| 55_T | 63_T | 1.114 | 0.77 |
| 449_L | 473_D | 1.114 | 0.77 |
| 456_F | 474_A | 1.112 | 0.77 |
| 450_S | 455_A | 1.111 | 0.77 |
| 115_F | 209_L | 1.111 | 0.77 |
| 450_S | 468_T | 1.109 | 0.77 |
| 449_L | 452_F | 1.108 | 0.77 |
| 236_T | 404_L | 1.107 | 0.76 |
| 344_V | 348_F | 1.104 | 0.76 |
| 369_F | 397_A | 1.104 | 0.76 |
| 452_F | 466_Y | 1.102 | 0.76 |
| 288_F | 291_R | 1.100 | 0.76 |
| 39_E | 43_H | 1.097 | 0.76 |
| 452_F | 462_L | 1.097 | 0.76 |
| 91_V | 143_N | 1.094 | 0.75 |
| 74_S | 235_V | 1.094 | 0.75 |
| 432_K | 439_L | 1.090 | 0.75 |
| 34_Y | 70_V | 1.088 | 0.75 |
| 442_A | 452_F | 1.088 | 0.75 |
| 29_N | 32_W | 1.087 | 0.75 |
| 466_Y | 472_A | 1.087 | 0.75 |
| 382_F | 386_R | 1.083 | 0.74 |
| 159_T | 233_A | 1.081 | 0.74 |
| 4_A | 8_V | 1.081 | 0.74 |
| 455_A | 475_Q | 1.079 | 0.74 |
| 461_A | 473_D | 1.078 | 0.74 |
| 315_F | 318_S | 1.075 | 0.73 |
| 457_A | 475_Q | 1.075 | 0.73 |
| 11_R | 14_N | 1.073 | 0.73 |
| 162_L | 165_N | 1.072 | 0.73 |
| 5_L | 9_K | 1.071 | 0.73 |
| 100_G | 103_A | 1.071 | 0.73 |
| 450_S | 456_F | 1.070 | 0.73 |
| 67_P | 71_Y | 1.067 | 0.73 |
| 432_K | 464_A | 1.067 | 0.73 |
| 109_L | 161_L | 1.066 | 0.73 |
| 106_P | 154_V | 1.064 | 0.72 |
| 312_G | 316_V | 1.064 | 0.72 |
| 108_Y | 155_S | 1.058 | 0.72 |
| 62_Y | 67_P | 1.056 | 0.72 |
| 255_S | 411_A | 1.055 | 0.71 |
| 73_G | 76_A | 1.054 | 0.71 |
| 4_A | 7_S | 1.054 | 0.71 |
| 460_I | 469_Y | 1.054 | 0.71 |
| 3_A | 14_N | 1.053 | 0.71 |
| 457_A | 472_A | 1.049 | 0.71 |
| 6_I | 9_K | 1.044 | 0.70 |
| 189_I | 236_T | 1.043 | 0.70 |
| 4_A | 11_R | 1.041 | 0.70 |
| 467_P | 473_D | 1.038 | 0.70 |
| 461_A | 472_A | 1.038 | 0.70 |
| 468_T | 475_Q | 1.037 | 0.70 |
| 7_S | 18_S | 1.037 | 0.70 |
| 339_L | 344_V | 1.037 | 0.70 |
| 216_F | 220_G | 1.036 | 0.69 |
| 417_V | 420_V | 1.035 | 0.69 |
| 441_N | 447_N | 1.035 | 0.69 |
| 4_A | 10_L | 1.034 | 0.69 |
| 453_R | 457_A | 1.032 | 0.69 |
| 456_F | 462_L | 1.032 | 0.69 |
| 454_V | 459_L | 1.030 | 0.69 |
| 145_H | 149_E | 1.029 | 0.69 |
| 451_Y | 461_A | 1.025 | 0.68 |
| 183_Y | 187_A | 1.023 | 0.68 |
| 459_L | 462_L | 1.022 | 0.68 |
| 77_G | 80_F | 1.021 | 0.68 |
| 92_L | 140_L | 1.021 | 0.68 |
| 451_Y | 464_A | 1.021 | 0.68 |
| 17_N | 23_T | 1.020 | 0.68 |
| 446_R | 452_F | 1.019 | 0.68 |
| 295_G | 299_M | 1.018 | 0.68 |
| 432_K | 435_L | 1.017 | 0.67 |
| 226_R | 229_L | 1.017 | 0.67 |
| 255_S | 260_S | 1.011 | 0.67 |
| 451_Y | 462_L | 1.011 | 0.67 |
| 120_A | 125_F | 1.011 | 0.67 |
| 472_A | 475_Q | 1.008 | 0.66 |
| 446_R | 450_S | 1.008 | 0.66 |
| 435_L | 438_A | 1.007 | 0.66 |
| 329_V | 354_E | 1.006 | 0.66 |
| 463_A | 473_D | 1.006 | 0.66 |
| 439_L | 457_A | 1.006 | 0.66 |
| 448_K | 459_L | 1.006 | 0.66 |
| 434_H | 437_R | 1.005 | 0.66 |
| 459_L | 475_Q | 1.005 | 0.66 |
| 36_R | 40_N | 1.004 | 0.66 |
| 307_T | 310_I | 1.003 | 0.66 |
| 459_L | 474_A | 1.003 | 0.66 |
| 108_Y | 112_R | 1.003 | 0.66 |
| 451_Y | 469_Y | 1.001 | 0.66 |
| 435_L | 442_A | 1.001 | 0.66 |
| 5_L | 8_V | 1.001 | 0.66 |
| 207_I | 212_M | 1.001 | 0.66 |
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 | |
| 3wajA | 1 | 0.8887 | 100 | 0.369 | Contact Map |
| 3rceA | 1 | 0.8445 | 100 | 0.39 | Contact Map |
| 2zaiA | 4 | 0.0777 | 99.8 | 0.777 | Contact Map |
| 2lgzA | 1 | 0.1933 | 99.7 | 0.789 | Contact Map |
| 3vu0A | 3 | 0.1092 | 99.3 | 0.847 | Contact Map |
| 3vgpA | 1 | 0.1092 | 99.2 | 0.848 | Contact Map |
| 3lfkA | 4 | 0.1639 | 3.2 | 0.977 | Contact Map |
| 3i9v7 | 2 | 0.1092 | 2.5 | 0.978 | Contact Map |
| 4xedA | 1 | 0 | 2.2 | 0.979 | Contact Map |
| 2ksfA | 1 | 0.2185 | 1.6 | 0.98 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)