| acchemei |
| ID: | 1456111584 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 445 (385) | ||
| Sequences: | 9512 (5327.4) | ||
| Seq/Len: | 24.706 | ||
| Nf(neff/√len): | 271.5 |
HHblits Results: (2015_06)
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: 24.706).
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 |
| 188_E | 231_R | 3.893 | 1.00 |
| 75_E | 85_F | 3.192 | 1.00 |
| 219_R | 223_E | 3.019 | 1.00 |
| 146_A | 168_K | 3.001 | 1.00 |
| 340_K | 344_E | 2.997 | 1.00 |
| 349_G | 429_D | 2.851 | 1.00 |
| 394_V | 433_R | 2.824 | 1.00 |
| 426_V | 429_D | 2.791 | 1.00 |
| 126_T | 132_A | 2.675 | 1.00 |
| 345_M | 425_H | 2.513 | 1.00 |
| 186_A | 189_E | 2.457 | 1.00 |
| 348_E | 352_T | 2.423 | 1.00 |
| 102_S | 106_S | 2.418 | 1.00 |
| 203_G | 237_V | 2.391 | 1.00 |
| 223_E | 227_D | 2.375 | 1.00 |
| 426_V | 430_R | 2.374 | 1.00 |
| 349_G | 352_T | 2.310 | 1.00 |
| 356_E | 369_N | 2.293 | 1.00 |
| 68_E | 72_E | 2.247 | 1.00 |
| 181_Q | 221_T | 2.198 | 1.00 |
| 389_R | 434_F | 2.181 | 1.00 |
| 145_D | 202_R | 2.166 | 1.00 |
| 349_G | 428_L | 2.159 | 1.00 |
| 389_R | 393_E | 2.158 | 1.00 |
| 188_E | 224_D | 2.129 | 1.00 |
| 151_T | 171_P | 2.119 | 1.00 |
| 108_M | 291_Y | 2.084 | 1.00 |
| 432_R | 436_E | 2.080 | 1.00 |
| 292_S | 298_V | 2.058 | 1.00 |
| 226_L | 230_T | 2.052 | 1.00 |
| 184_P | 228_F | 2.047 | 1.00 |
| 349_G | 432_R | 2.036 | 1.00 |
| 76_G | 86_R | 2.027 | 1.00 |
| 129_A | 273_V | 2.001 | 1.00 |
| 136_L | 271_H | 1.995 | 1.00 |
| 108_M | 289_T | 1.939 | 1.00 |
| 229_V | 234_I | 1.907 | 1.00 |
| 191_Y | 228_F | 1.905 | 1.00 |
| 141_A | 167_V | 1.895 | 1.00 |
| 188_E | 192_N | 1.892 | 1.00 |
| 290_I | 301_A | 1.892 | 1.00 |
| 398_I | 412_F | 1.880 | 1.00 |
| 137_T | 205_L | 1.868 | 1.00 |
| 347_I | 351_R | 1.830 | 1.00 |
| 229_V | 236_L | 1.820 | 1.00 |
| 188_E | 232_K | 1.810 | 1.00 |
| 104_M | 125_L | 1.788 | 1.00 |
| 180_F | 356_E | 1.788 | 1.00 |
| 311_S | 314_T | 1.787 | 1.00 |
| 341_K | 421_E | 1.783 | 1.00 |
| 122_R | 267_A | 1.773 | 1.00 |
| 140_L | 271_H | 1.747 | 1.00 |
| 347_I | 366_C | 1.741 | 1.00 |
| 241_I | 275_S | 1.738 | 1.00 |
| 345_M | 420_S | 1.738 | 1.00 |
| 346_I | 424_L | 1.719 | 1.00 |
| 346_I | 428_L | 1.710 | 1.00 |
| 140_L | 203_G | 1.705 | 1.00 |
| 233_N | 269_R | 1.702 | 1.00 |
| 345_M | 349_G | 1.679 | 1.00 |
| 54_M | 427_A | 1.677 | 1.00 |
| 218_Q | 221_T | 1.670 | 1.00 |
| 186_A | 190_A | 1.668 | 1.00 |
| 189_E | 193_S | 1.666 | 1.00 |
| 351_R | 357_C | 1.654 | 1.00 |
| 338_R | 341_K | 1.637 | 1.00 |
| 185_K | 224_D | 1.628 | 1.00 |
| 103_A | 323_S | 1.620 | 1.00 |
| 178_N | 186_A | 1.619 | 1.00 |
| 69_Y | 320_S | 1.615 | 1.00 |
| 140_L | 235_H | 1.608 | 1.00 |
| 98_F | 102_S | 1.598 | 1.00 |
| 352_T | 432_R | 1.586 | 1.00 |
| 95_H | 101_R | 1.585 | 1.00 |
| 333_K | 337_D | 1.585 | 1.00 |
| 341_K | 420_S | 1.580 | 1.00 |
| 99_S | 319_A | 1.575 | 1.00 |
| 161_L | 167_V | 1.569 | 1.00 |
| 146_A | 201_V | 1.566 | 1.00 |
| 109_E | 115_R | 1.555 | 1.00 |
| 274_Y | 289_T | 1.553 | 1.00 |
| 422_K | 425_H | 1.553 | 1.00 |
| 227_D | 230_T | 1.551 | 1.00 |
| 353_A | 432_R | 1.535 | 1.00 |
| 72_E | 85_F | 1.524 | 1.00 |
| 146_A | 199_I | 1.520 | 1.00 |
| 375_K | 385_E | 1.516 | 1.00 |
| 104_M | 123_V | 1.508 | 1.00 |
| 337_D | 341_K | 1.507 | 1.00 |
| 230_T | 264_Y | 1.507 | 1.00 |
| 97_L | 316_R | 1.501 | 1.00 |
| 134_E | 138_F | 1.498 | 1.00 |
| 190_A | 199_I | 1.494 | 1.00 |
| 184_P | 224_D | 1.488 | 1.00 |
| 175_D | 179_N | 1.475 | 1.00 |
| 192_N | 231_R | 1.474 | 1.00 |
| 349_G | 425_H | 1.459 | 1.00 |
| 394_V | 437_R | 1.458 | 1.00 |
| 419_M | 423_T | 1.455 | 1.00 |
| 394_V | 430_R | 1.455 | 1.00 |
| 105_G | 123_V | 1.450 | 1.00 |
| 220_S | 223_E | 1.441 | 1.00 |
| 106_S | 110_E | 1.426 | 1.00 |
| 187_L | 225_I | 1.421 | 1.00 |
| 107_F | 112_R | 1.417 | 1.00 |
| 51_V | 395_K | 1.413 | 1.00 |
| 151_T | 173_H | 1.403 | 0.99 |
| 224_D | 227_D | 1.398 | 0.99 |
| 182_I | 187_L | 1.385 | 0.99 |
| 219_R | 253_T | 1.383 | 0.99 |
| 346_I | 366_C | 1.379 | 0.99 |
| 385_E | 389_R | 1.378 | 0.99 |
| 355_I | 368_M | 1.372 | 0.99 |
| 287_V | 318_L | 1.372 | 0.99 |
| 101_R | 105_G | 1.363 | 0.99 |
| 183_T | 186_A | 1.344 | 0.99 |
| 300_T | 303_R | 1.325 | 0.99 |
| 347_I | 359_E | 1.321 | 0.99 |
| 333_K | 336_R | 1.320 | 0.99 |
| 221_T | 224_D | 1.317 | 0.99 |
| 276_L | 318_L | 1.314 | 0.99 |
| 429_D | 433_R | 1.309 | 0.99 |
| 112_R | 243_S | 1.307 | 0.99 |
| 175_D | 178_N | 1.305 | 0.99 |
| 137_T | 141_A | 1.300 | 0.99 |
| 123_V | 291_Y | 1.294 | 0.99 |
| 394_V | 434_F | 1.292 | 0.99 |
| 344_E | 348_E | 1.278 | 0.99 |
| 118_F | 291_Y | 1.277 | 0.99 |
| 104_M | 289_T | 1.274 | 0.99 |
| 124_V | 298_V | 1.272 | 0.99 |
| 149_V | 161_L | 1.261 | 0.99 |
| 52_I | 419_M | 1.258 | 0.99 |
| 334_M | 337_D | 1.257 | 0.99 |
| 271_H | 292_S | 1.253 | 0.99 |
| 390_I | 431_I | 1.247 | 0.99 |
| 175_D | 186_A | 1.244 | 0.98 |
| 396_L | 431_I | 1.243 | 0.98 |
| 393_E | 437_R | 1.243 | 0.98 |
| 390_I | 434_F | 1.237 | 0.98 |
| 219_R | 251_E | 1.228 | 0.98 |
| 141_A | 203_G | 1.222 | 0.98 |
| 109_E | 117_K | 1.207 | 0.98 |
| 111_I | 244_G | 1.204 | 0.98 |
| 68_E | 71_E | 1.199 | 0.98 |
| 237_V | 273_V | 1.197 | 0.98 |
| 388_K | 392_K | 1.194 | 0.98 |
| 88_N | 316_R | 1.191 | 0.98 |
| 216_T | 253_T | 1.176 | 0.98 |
| 107_F | 111_I | 1.176 | 0.98 |
| 147_L | 161_L | 1.171 | 0.98 |
| 220_S | 224_D | 1.171 | 0.98 |
| 132_A | 290_I | 1.169 | 0.97 |
| 136_L | 237_V | 1.165 | 0.97 |
| 398_I | 414_V | 1.162 | 0.97 |
| 287_V | 310_I | 1.159 | 0.97 |
| 219_R | 257_E | 1.144 | 0.97 |
| 141_A | 147_L | 1.137 | 0.97 |
| 147_L | 203_G | 1.135 | 0.97 |
| 148_L | 190_A | 1.133 | 0.97 |
| 102_S | 105_G | 1.131 | 0.97 |
| 129_A | 241_I | 1.128 | 0.97 |
| 348_E | 351_R | 1.126 | 0.97 |
| 349_G | 353_A | 1.124 | 0.97 |
| 107_F | 243_S | 1.124 | 0.97 |
| 146_A | 170_V | 1.120 | 0.96 |
| 356_E | 372_P | 1.118 | 0.96 |
| 206_I | 225_I | 1.115 | 0.96 |
| 323_S | 329_E | 1.115 | 0.96 |
| 245_S | 336_R | 1.108 | 0.96 |
| 176_S | 369_N | 1.106 | 0.96 |
| 287_V | 314_T | 1.090 | 0.96 |
| 185_K | 189_E | 1.089 | 0.96 |
| 72_E | 76_G | 1.087 | 0.96 |
| 240_E | 254_S | 1.084 | 0.96 |
| 390_I | 398_I | 1.079 | 0.95 |
| 347_I | 357_C | 1.064 | 0.95 |
| 337_D | 340_K | 1.063 | 0.95 |
| 139_I | 301_A | 1.057 | 0.95 |
| 226_L | 270_V | 1.053 | 0.95 |
| 107_F | 280_L | 1.051 | 0.94 |
| 71_E | 75_E | 1.045 | 0.94 |
| 95_H | 302_R | 1.040 | 0.94 |
| 250_D | 340_K | 1.039 | 0.94 |
| 143_P | 166_G | 1.035 | 0.94 |
| 149_V | 169_I | 1.028 | 0.94 |
| 170_V | 199_I | 1.025 | 0.93 |
| 191_Y | 234_I | 1.024 | 0.93 |
| 50_G | 395_K | 1.023 | 0.93 |
| 103_A | 106_S | 1.022 | 0.93 |
| 228_F | 232_K | 1.019 | 0.93 |
| 147_L | 169_I | 1.012 | 0.93 |
| 256_A | 272_I | 1.009 | 0.93 |
| 387_W | 398_I | 1.009 | 0.93 |
| 204_V | 229_V | 1.008 | 0.93 |
| 148_L | 201_V | 1.007 | 0.93 |
| 271_H | 297_V | 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
- 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 | |
| 3piuA | 1 | 0.9079 | 100 | 0.315 | Contact Map |
| 1iayA | 1 | 0.9348 | 100 | 0.332 | Contact Map |
| 3dydA | 2 | 0.8427 | 100 | 0.413 | Contact Map |
| 2x5dA | 4 | 0.8472 | 100 | 0.418 | Contact Map |
| 1gd9A | 2 | 0.8652 | 100 | 0.419 | Contact Map |
| 1yizA | 2 | 0.8742 | 100 | 0.419 | Contact Map |
| 3e2yA | 2 | 0.8652 | 100 | 0.419 | Contact Map |
| 1vp4A | 2 | 0.8966 | 100 | 0.423 | Contact Map |
| 2o1bA | 1 | 0.836 | 100 | 0.423 | Contact Map |
| 4my5A | 4 | 0.8697 | 100 | 0.425 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)