| ftsw_1 |
| ID: | 1489159033 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 414 (374) | ||
| Sequences: | 4579 (3245.2) | ||
| Seq/Len: | 12.243 | ||
| Nf(neff/√len): | 167.8 |
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: 12.243).
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 |
| 45_D | 325_R | 4.516 | 1.00 |
| 326_A | 349_G | 4.201 | 1.00 |
| 345_A | 394_L | 3.357 | 1.00 |
| 77_D | 83_K | 3.180 | 1.00 |
| 326_A | 394_L | 3.145 | 1.00 |
| 271_F | 304_G | 3.057 | 1.00 |
| 104_M | 341_S | 3.046 | 1.00 |
| 140_D | 143_L | 2.776 | 1.00 |
| 256_D | 259_G | 2.723 | 1.00 |
| 131_S | 136_S | 2.647 | 1.00 |
| 376_L | 391_I | 2.631 | 1.00 |
| 252_N | 255_E | 2.594 | 1.00 |
| 210_A | 350_I | 2.555 | 1.00 |
| 304_G | 312_V | 2.554 | 1.00 |
| 214_L | 346_C | 2.488 | 1.00 |
| 323_A | 353_S | 2.474 | 1.00 |
| 118_S | 155_S | 2.420 | 1.00 |
| 293_E | 296_T | 2.401 | 1.00 |
| 96_A | 395_L | 2.300 | 1.00 |
| 56_A | 89_L | 2.219 | 1.00 |
| 92_A | 388_S | 2.202 | 1.00 |
| 52_T | 391_I | 2.187 | 1.00 |
| 300_F | 312_V | 2.176 | 1.00 |
| 99_T | 389_T | 2.168 | 1.00 |
| 348_I | 394_L | 2.161 | 1.00 |
| 51_L | 321_F | 2.090 | 1.00 |
| 361_G | 367_L | 2.086 | 1.00 |
| 316_L | 360_V | 2.080 | 1.00 |
| 362_A | 369_T | 2.049 | 1.00 |
| 281_L | 307_L | 2.026 | 1.00 |
| 114_M | 155_S | 1.979 | 1.00 |
| 51_L | 322_V | 1.977 | 1.00 |
| 133_K | 293_E | 1.955 | 1.00 |
| 51_L | 318_M | 1.899 | 1.00 |
| 211_M | 347_S | 1.866 | 1.00 |
| 341_S | 397_I | 1.861 | 1.00 |
| 62_M | 303_I | 1.847 | 1.00 |
| 376_L | 387_M | 1.840 | 1.00 |
| 122_L | 152_T | 1.823 | 1.00 |
| 62_M | 307_L | 1.823 | 1.00 |
| 118_S | 152_T | 1.791 | 1.00 |
| 203_V | 372_L | 1.786 | 1.00 |
| 140_D | 145_R | 1.779 | 1.00 |
| 254_W | 265_T | 1.772 | 1.00 |
| 313_V | 317_L | 1.746 | 1.00 |
| 157_F | 347_S | 1.719 | 1.00 |
| 146_I | 151_L | 1.712 | 1.00 |
| 88_Y | 381_G | 1.703 | 1.00 |
| 356_A | 360_V | 1.688 | 1.00 |
| 303_I | 315_A | 1.674 | 1.00 |
| 333_A | 397_I | 1.670 | 1.00 |
| 284_S | 302_I | 1.652 | 1.00 |
| 110_Y | 113_T | 1.628 | 1.00 |
| 241_P | 244_I | 1.619 | 1.00 |
| 345_A | 397_I | 1.616 | 1.00 |
| 60_F | 82_A | 1.612 | 1.00 |
| 158_C | 344_L | 1.612 | 1.00 |
| 149_A | 200_T | 1.601 | 1.00 |
| 95_L | 389_T | 1.590 | 1.00 |
| 298_F | 369_T | 1.576 | 1.00 |
| 160_I | 208_T | 1.555 | 1.00 |
| 80_F | 84_R | 1.542 | 1.00 |
| 58_I | 303_I | 1.541 | 1.00 |
| 58_I | 318_M | 1.534 | 1.00 |
| 373_T | 383_S | 1.534 | 1.00 |
| 300_F | 360_V | 1.531 | 1.00 |
| 120_I | 124_I | 1.511 | 1.00 |
| 91_L | 385_L | 1.498 | 1.00 |
| 349_G | 394_L | 1.493 | 1.00 |
| 257_P | 265_T | 1.491 | 1.00 |
| 309_Y | 313_V | 1.470 | 1.00 |
| 61_I | 281_L | 1.465 | 1.00 |
| 108_Q | 340_F | 1.459 | 1.00 |
| 240_E | 243_R | 1.456 | 1.00 |
| 264_L | 365_G | 1.455 | 1.00 |
| 338_H | 341_S | 1.451 | 1.00 |
| 157_F | 351_W | 1.441 | 1.00 |
| 151_L | 386_I | 1.439 | 1.00 |
| 56_A | 388_S | 1.436 | 1.00 |
| 190_V | 194_A | 1.434 | 1.00 |
| 124_I | 128_V | 1.432 | 1.00 |
| 60_F | 85_D | 1.420 | 1.00 |
| 161_A | 211_M | 1.418 | 1.00 |
| 55_L | 377_I | 1.418 | 1.00 |
| 277_W | 310_V | 1.412 | 1.00 |
| 348_I | 390_A | 1.407 | 0.99 |
| 116_L | 120_I | 1.402 | 0.99 |
| 264_L | 369_T | 1.400 | 0.99 |
| 303_I | 377_I | 1.384 | 0.99 |
| 352_F | 387_M | 1.384 | 0.99 |
| 119_I | 123_M | 1.383 | 0.99 |
| 266_Q | 269_M | 1.380 | 0.99 |
| 48_L | 322_V | 1.379 | 0.99 |
| 48_L | 329_I | 1.378 | 0.99 |
| 207_T | 351_W | 1.376 | 0.99 |
| 157_F | 207_T | 1.373 | 0.99 |
| 206_V | 354_F | 1.373 | 0.99 |
| 245_R | 260_S | 1.366 | 0.99 |
| 92_A | 392_M | 1.362 | 0.99 |
| 96_A | 392_M | 1.346 | 0.99 |
| 125_V | 139_I | 1.333 | 0.99 |
| 130_S | 140_D | 1.331 | 0.99 |
| 211_M | 343_F | 1.326 | 0.99 |
| 81_F | 295_H | 1.322 | 0.99 |
| 65_S | 306_E | 1.322 | 0.99 |
| 102_L | 107_W | 1.316 | 0.99 |
| 276_L | 309_Y | 1.314 | 0.99 |
| 344_L | 397_I | 1.306 | 0.99 |
| 158_C | 340_F | 1.304 | 0.99 |
| 115_L | 188_L | 1.302 | 0.99 |
| 150_E | 153_K | 1.300 | 0.99 |
| 62_M | 299_I | 1.289 | 0.99 |
| 66_A | 302_I | 1.285 | 0.99 |
| 262_Y | 266_Q | 1.280 | 0.99 |
| 58_I | 315_A | 1.271 | 0.99 |
| 261_G | 265_T | 1.269 | 0.99 |
| 162_N | 166_R | 1.266 | 0.99 |
| 106_F | 109_R | 1.248 | 0.99 |
| 94_I | 98_I | 1.239 | 0.98 |
| 326_A | 345_A | 1.234 | 0.98 |
| 396_R | 400_E | 1.231 | 0.98 |
| 183_G | 187_V | 1.227 | 0.98 |
| 256_D | 260_S | 1.222 | 0.98 |
| 199_G | 370_K | 1.212 | 0.98 |
| 267_S | 363_A | 1.198 | 0.98 |
| 328_S | 332_K | 1.185 | 0.98 |
| 266_Q | 286_Q | 1.180 | 0.98 |
| 164_L | 215_A | 1.167 | 0.97 |
| 104_M | 396_R | 1.167 | 0.97 |
| 210_A | 354_F | 1.162 | 0.97 |
| 218_K | 221_Q | 1.159 | 0.97 |
| 55_L | 315_A | 1.155 | 0.97 |
| 52_T | 388_S | 1.154 | 0.97 |
| 296_T | 379_Y | 1.151 | 0.97 |
| 146_I | 382_S | 1.138 | 0.97 |
| 323_A | 356_A | 1.134 | 0.97 |
| 244_I | 248_T | 1.134 | 0.97 |
| 54_G | 318_M | 1.132 | 0.97 |
| 197_D | 200_T | 1.123 | 0.97 |
| 137_R | 149_A | 1.120 | 0.96 |
| 104_M | 338_H | 1.117 | 0.96 |
| 164_L | 211_M | 1.116 | 0.96 |
| 262_Y | 292_P | 1.107 | 0.96 |
| 273_R | 279_Q | 1.107 | 0.96 |
| 157_F | 211_M | 1.105 | 0.96 |
| 291_L | 301_A | 1.103 | 0.96 |
| 193_L | 201_V | 1.099 | 0.96 |
| 333_A | 337_D | 1.096 | 0.96 |
| 351_W | 390_A | 1.088 | 0.96 |
| 58_I | 62_M | 1.087 | 0.96 |
| 80_F | 83_K | 1.084 | 0.96 |
| 374_L | 377_I | 1.083 | 0.96 |
| 394_L | 397_I | 1.083 | 0.96 |
| 355_Q | 373_T | 1.079 | 0.95 |
| 83_K | 86_G | 1.078 | 0.95 |
| 96_A | 99_T | 1.075 | 0.95 |
| 284_S | 306_E | 1.070 | 0.95 |
| 111_S | 340_F | 1.069 | 0.95 |
| 316_L | 356_A | 1.062 | 0.95 |
| 298_F | 363_A | 1.056 | 0.95 |
| 125_V | 129_G | 1.055 | 0.95 |
| 213_F | 219_L | 1.052 | 0.95 |
| 267_S | 298_F | 1.050 | 0.94 |
| 163_Y | 181_P | 1.042 | 0.94 |
| 64_T | 82_A | 1.039 | 0.94 |
| 177_G | 180_K | 1.038 | 0.94 |
| 135_A | 195_Q | 1.037 | 0.94 |
| 276_L | 310_V | 1.031 | 0.94 |
| 107_W | 393_M | 1.030 | 0.94 |
| 137_R | 199_G | 1.028 | 0.94 |
| 264_L | 267_S | 1.025 | 0.93 |
| 198_L | 202_V | 1.024 | 0.93 |
| 345_A | 349_G | 1.022 | 0.93 |
| 132_V | 145_R | 1.020 | 0.93 |
| 279_Q | 285_V | 1.017 | 0.93 |
| 339_R | 342_G | 1.016 | 0.93 |
| 100_L | 392_M | 1.011 | 0.93 |
| 253_P | 261_G | 1.011 | 0.93 |
| 161_A | 165_V | 1.010 | 0.93 |
| 103_P | 341_S | 1.009 | 0.93 |
| 123_M | 127_V | 1.005 | 0.93 |
| 112_A | 159_Y | 1.001 | 0.92 |
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 | |
| 4x5mA | 3 | 0.2271 | 4 | 0.978 | Contact Map |
| 4qncA | 2 | 0.1836 | 2.9 | 0.98 | Contact Map |
| 2kv9B | 1 | 0.0725 | 2.3 | 0.981 | Contact Map |
| 4ogqE | 1 | 0.0749 | 2.1 | 0.981 | Contact Map |
| 2m20A | 2 | 0.099 | 2 | 0.981 | Contact Map |
| 1q16C | 1 | 0.2585 | 2 | 0.981 | Contact Map |
| 4i7zE | 1 | 0.0676 | 1.8 | 0.982 | Contact Map |
| 2k9jB | 1 | 0.1039 | 1.8 | 0.982 | Contact Map |
| 1pfiA | 2 | 0.1111 | 1.8 | 0.982 | Contact Map |
| 2kogA | 1 | 0.1498 | 1.7 | 0.982 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)