| sub_bpn |
| ID: | 1494273959 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 405 (363) | ||
| Sequences: | 7229 (5104.1) | ||
| Seq/Len: | 19.915 | ||
| Nf(neff/√len): | 267.9 |
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: 19.915).
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 |
| 103_D | 215_S | 3.498 | 1.00 |
| 334_W | 342_N | 3.415 | 1.00 |
| 134_V | 182_V | 3.371 | 1.00 |
| 304_A | 312_P | 3.342 | 1.00 |
| 303_S | 324_A | 2.997 | 1.00 |
| 334_W | 344_I | 2.958 | 1.00 |
| 206_L | 212_G | 2.950 | 1.00 |
| 237_N | 351_S | 2.866 | 1.00 |
| 171_D | 208_G | 2.826 | 1.00 |
| 128_K | 197_A | 2.699 | 1.00 |
| 180_G | 332_S | 2.691 | 1.00 |
| 177_H | 349_M | 2.645 | 1.00 |
| 312_P | 328_V | 2.644 | 1.00 |
| 130_A | 197_A | 2.637 | 1.00 |
| 33_T | 103_D | 2.566 | 1.00 |
| 314_W | 328_V | 2.554 | 1.00 |
| 178_V | 237_N | 2.533 | 1.00 |
| 203_V | 220_G | 2.530 | 1.00 |
| 180_G | 333_T | 2.438 | 1.00 |
| 184_A | 333_T | 2.421 | 1.00 |
| 177_H | 332_S | 2.402 | 1.00 |
| 306_N | 328_V | 2.345 | 1.00 |
| 267_Q | 298_E | 2.287 | 1.00 |
| 170_D | 173_G | 2.231 | 1.00 |
| 133_S | 201_W | 2.229 | 1.00 |
| 136_V | 182_V | 2.168 | 1.00 |
| 260_D | 264_N | 2.150 | 1.00 |
| 37_V | 98_Y | 2.092 | 1.00 |
| 351_S | 355_A | 2.092 | 1.00 |
| 181_T | 353_H | 2.082 | 1.00 |
| 225_I | 269_A | 2.036 | 1.00 |
| 183_A | 198_A | 2.027 | 1.00 |
| 183_A | 200_L | 2.027 | 1.00 |
| 133_S | 199_E | 2.026 | 1.00 |
| 358_A | 373_V | 2.015 | 1.00 |
| 369_T | 372_Q | 2.012 | 1.00 |
| 141_I | 200_L | 2.009 | 1.00 |
| 39_E | 98_Y | 1.988 | 1.00 |
| 276_T | 358_A | 1.985 | 1.00 |
| 37_V | 99_A | 1.968 | 1.00 |
| 278_V | 351_S | 1.956 | 1.00 |
| 294_A | 301_T | 1.956 | 1.00 |
| 276_T | 300_I | 1.948 | 1.00 |
| 304_A | 314_W | 1.938 | 1.00 |
| 181_T | 349_M | 1.911 | 1.00 |
| 221_L | 269_A | 1.907 | 1.00 |
| 289_A | 320_D | 1.891 | 1.00 |
| 280_A | 351_S | 1.876 | 1.00 |
| 127_A | 363_S | 1.855 | 1.00 |
| 137_V | 205_V | 1.850 | 1.00 |
| 263_H | 295_A | 1.833 | 1.00 |
| 84_T | 87_Q | 1.819 | 1.00 |
| 269_A | 277_V | 1.765 | 1.00 |
| 306_N | 310_D | 1.757 | 1.00 |
| 106_V | 214_I | 1.742 | 1.00 |
| 375_A | 379_Q | 1.735 | 1.00 |
| 135_Y | 233_P | 1.728 | 1.00 |
| 357_A | 398_P | 1.726 | 1.00 |
| 304_A | 328_V | 1.718 | 1.00 |
| 285_G | 311_W | 1.700 | 1.00 |
| 374_K | 378_L | 1.691 | 1.00 |
| 365_Y | 376_F | 1.659 | 1.00 |
| 135_Y | 224_V | 1.655 | 1.00 |
| 309_D | 395_H | 1.652 | 1.00 |
| 134_V | 359_A | 1.645 | 1.00 |
| 303_S | 321_V | 1.640 | 1.00 |
| 203_V | 223_W | 1.630 | 1.00 |
| 382_E | 397_E | 1.616 | 1.00 |
| 323_L | 377_L | 1.604 | 1.00 |
| 311_W | 324_A | 1.597 | 1.00 |
| 101_T | 261_A | 1.597 | 1.00 |
| 357_A | 396_P | 1.595 | 1.00 |
| 142_K | 335_N | 1.594 | 1.00 |
| 223_W | 227_H | 1.592 | 1.00 |
| 267_Q | 272_D | 1.569 | 1.00 |
| 152_K | 199_E | 1.559 | 1.00 |
| 119_R | 309_D | 1.549 | 1.00 |
| 136_V | 178_V | 1.545 | 1.00 |
| 178_V | 352_P | 1.541 | 1.00 |
| 237_N | 355_A | 1.540 | 1.00 |
| 225_I | 275_I | 1.535 | 1.00 |
| 132_V | 362_L | 1.492 | 1.00 |
| 149_T | 185_V | 1.487 | 1.00 |
| 134_V | 198_A | 1.485 | 1.00 |
| 218_V | 265_V | 1.481 | 1.00 |
| 278_V | 358_A | 1.480 | 1.00 |
| 365_Y | 368_Y | 1.469 | 1.00 |
| 116_G | 353_H | 1.451 | 1.00 |
| 267_Q | 297_D | 1.451 | 1.00 |
| 68_A | 219_Q | 1.448 | 1.00 |
| 109_Y | 280_A | 1.437 | 1.00 |
| 304_A | 327_G | 1.432 | 1.00 |
| 284_E | 291_H | 1.417 | 1.00 |
| 276_T | 373_V | 1.402 | 0.99 |
| 218_V | 261_A | 1.401 | 0.99 |
| 331_L | 343_T | 1.400 | 0.99 |
| 222_N | 226_T | 1.399 | 0.99 |
| 88_A | 92_A | 1.396 | 0.99 |
| 362_L | 373_V | 1.381 | 0.99 |
| 205_V | 240_L | 1.379 | 0.99 |
| 205_V | 220_G | 1.375 | 0.99 |
| 179_A | 202_A | 1.373 | 0.99 |
| 266_I | 299_V | 1.365 | 0.99 |
| 305_T | 324_A | 1.358 | 0.99 |
| 368_Y | 376_F | 1.346 | 0.99 |
| 267_Q | 296_Y | 1.344 | 0.99 |
| 361_V | 368_Y | 1.329 | 0.99 |
| 213_S | 216_G | 1.327 | 0.99 |
| 332_S | 349_M | 1.327 | 0.99 |
| 235_V | 355_A | 1.322 | 0.99 |
| 268_K | 272_D | 1.322 | 0.99 |
| 234_K | 362_L | 1.321 | 0.99 |
| 201_W | 233_P | 1.320 | 0.99 |
| 33_T | 82_N | 1.319 | 0.99 |
| 278_V | 355_A | 1.318 | 0.99 |
| 302_V | 323_L | 1.317 | 0.99 |
| 132_V | 359_A | 1.305 | 0.99 |
| 128_K | 363_S | 1.297 | 0.99 |
| 344_I | 349_M | 1.295 | 0.99 |
| 280_A | 350_A | 1.287 | 0.99 |
| 101_T | 259_T | 1.284 | 0.99 |
| 147_D | 333_T | 1.278 | 0.99 |
| 300_I | 374_K | 1.276 | 0.99 |
| 194_V | 356_G | 1.270 | 0.99 |
| 263_H | 267_Q | 1.255 | 0.99 |
| 217_I | 240_L | 1.254 | 0.99 |
| 236_V | 277_V | 1.242 | 0.98 |
| 141_I | 179_A | 1.241 | 0.98 |
| 357_A | 377_L | 1.229 | 0.98 |
| 376_F | 380_N | 1.219 | 0.98 |
| 177_H | 181_T | 1.216 | 0.98 |
| 326_P | 330_I | 1.199 | 0.98 |
| 142_K | 338_T | 1.197 | 0.98 |
| 278_V | 354_V | 1.197 | 0.98 |
| 142_K | 336_A | 1.194 | 0.98 |
| 236_V | 269_A | 1.193 | 0.98 |
| 177_H | 344_I | 1.178 | 0.98 |
| 143_V | 151_L | 1.175 | 0.98 |
| 358_A | 377_L | 1.168 | 0.97 |
| 311_W | 317_Y | 1.163 | 0.97 |
| 139_T | 172_N | 1.161 | 0.97 |
| 108_A | 206_L | 1.161 | 0.97 |
| 214_I | 262_F | 1.158 | 0.97 |
| 239_S | 352_P | 1.152 | 0.97 |
| 156_A | 159_K | 1.139 | 0.97 |
| 104_R | 214_I | 1.139 | 0.97 |
| 151_L | 202_A | 1.134 | 0.97 |
| 59_E | 64_L | 1.120 | 0.96 |
| 137_V | 220_G | 1.109 | 0.96 |
| 97_V | 100_L | 1.101 | 0.96 |
| 221_L | 266_I | 1.101 | 0.96 |
| 302_V | 354_V | 1.100 | 0.96 |
| 153_G | 201_W | 1.099 | 0.96 |
| 305_T | 309_D | 1.095 | 0.96 |
| 371_A | 375_A | 1.092 | 0.96 |
| 284_E | 316_N | 1.090 | 0.96 |
| 156_A | 204_K | 1.088 | 0.96 |
| 296_Y | 299_V | 1.085 | 0.96 |
| 314_W | 345_S | 1.080 | 0.95 |
| 176_T | 333_T | 1.075 | 0.95 |
| 236_V | 275_I | 1.073 | 0.95 |
| 38_L | 79_I | 1.071 | 0.95 |
| 141_I | 148_L | 1.070 | 0.95 |
| 311_W | 315_S | 1.069 | 0.95 |
| 120_I | 194_V | 1.060 | 0.95 |
| 323_L | 396_P | 1.054 | 0.95 |
| 152_K | 201_W | 1.049 | 0.94 |
| 336_A | 340_S | 1.046 | 0.94 |
| 383_S | 388_Q | 1.043 | 0.94 |
| 322_D | 378_L | 1.039 | 0.94 |
| 212_G | 216_G | 1.033 | 0.94 |
| 39_E | 96_R | 1.029 | 0.94 |
| 221_L | 238_M | 1.024 | 0.93 |
| 303_S | 315_S | 1.023 | 0.93 |
| 221_L | 236_V | 1.022 | 0.93 |
| 195_A | 359_A | 1.021 | 0.93 |
| 145_H | 341_Y | 1.020 | 0.93 |
| 222_N | 268_K | 1.005 | 0.93 |
| 317_Y | 390_T | 1.004 | 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 | |
| 3whiA | 2 | 0.842 | 100 | 0.216 | Contact Map |
| 3wiuA | 3 | 0.8469 | 100 | 0.249 | Contact Map |
| 3afgA | 2 | 0.9037 | 100 | 0.255 | Contact Map |
| 1r6vA | 1 | 0.9012 | 100 | 0.255 | Contact Map |
| 2p4eP | 2 | 0.8568 | 100 | 0.256 | Contact Map |
| 3t41A | 2 | 0.8691 | 100 | 0.257 | Contact Map |
| 4tr2A | 2 | 0.8296 | 100 | 0.307 | Contact Map |
| 2x8jA | 5 | 0.7259 | 100 | 0.34 | Contact Map |
| 4mzdA | 1 | 0.6519 | 100 | 0.34 | Contact Map |
| 1to2E | 1 | 0.6691 | 100 | 0.34 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)