| 3mkt |
| ID: | 1408345796 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 460 (433) | ||
| Sequences: | 14514 (11910.3) | ||
| Seq/Len: | 33.520 | ||
| Nf(neff/√len): | 572.4 |
HHblits Results: (2013_03)
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: 33.520).
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 |
| 83_R | 86_K | 4.186 | 1.00 |
| 309_D | 312_G | 3.835 | 1.00 |
| 238_I | 242_R | 3.564 | 1.00 |
| 51_S | 277_Q | 3.483 | 1.00 |
| 158_L | 161_P | 3.345 | 1.00 |
| 142_A | 204_W | 3.063 | 1.00 |
| 420_G | 423_G | 2.671 | 1.00 |
| 338_F | 341_Q | 2.623 | 1.00 |
| 343_A | 356_A | 2.614 | 1.00 |
| 111_Q | 114_F | 2.608 | 1.00 |
| 76_A | 302_G | 2.502 | 1.00 |
| 130_V | 134_H | 2.352 | 1.00 |
| 339_R | 357_M | 2.336 | 1.00 |
| 339_R | 361_L | 2.235 | 1.00 |
| 131_G | 193_V | 2.202 | 1.00 |
| 12_S | 16_K | 2.194 | 1.00 |
| 385_D | 442_R | 2.172 | 1.00 |
| 113_Q | 130_V | 2.139 | 1.00 |
| 275_A | 355_L | 2.092 | 1.00 |
| 385_D | 388_A | 2.080 | 1.00 |
| 304_K | 312_G | 2.058 | 1.00 |
| 71_L | 94_G | 2.038 | 1.00 |
| 49_A | 128_K | 2.034 | 1.00 |
| 89_F | 233_Q | 1.939 | 1.00 |
| 135_A | 196_G | 1.906 | 1.00 |
| 78_L | 86_K | 1.900 | 1.00 |
| 160_K | 164_V | 1.890 | 1.00 |
| 234_P | 238_I | 1.886 | 1.00 |
| 336_V | 361_L | 1.878 | 1.00 |
| 369_M | 433_S | 1.853 | 1.00 |
| 165_I | 210_L | 1.833 | 1.00 |
| 317_A | 376_A | 1.815 | 1.00 |
| 43_S | 46_D | 1.800 | 1.00 |
| 165_I | 209_L | 1.792 | 1.00 |
| 138_F | 141_P | 1.781 | 1.00 |
| 423_G | 427_G | 1.778 | 1.00 |
| 38_M | 178_W | 1.772 | 1.00 |
| 357_M | 361_L | 1.768 | 1.00 |
| 135_A | 193_V | 1.761 | 1.00 |
| 172_L | 205_I | 1.747 | 1.00 |
| 419_L | 426_L | 1.741 | 1.00 |
| 387_T | 391_H | 1.705 | 1.00 |
| 318_N | 322_M | 1.697 | 1.00 |
| 142_A | 207_L | 1.694 | 1.00 |
| 35_D | 173_N | 1.694 | 1.00 |
| 317_A | 379_S | 1.688 | 1.00 |
| 340_E | 344_L | 1.687 | 1.00 |
| 157_S | 303_H | 1.673 | 1.00 |
| 305_L | 313_A | 1.666 | 1.00 |
| 22_L | 292_S | 1.666 | 1.00 |
| 261_V | 276_H | 1.665 | 1.00 |
| 38_M | 181_V | 1.658 | 1.00 |
| 75_V | 155_G | 1.648 | 1.00 |
| 139_A | 200_A | 1.641 | 1.00 |
| 79_N | 87_I | 1.634 | 1.00 |
| 315_I | 319_V | 1.631 | 1.00 |
| 297_V | 320_G | 1.621 | 1.00 |
| 113_Q | 117_R | 1.613 | 1.00 |
| 145_L | 207_L | 1.612 | 1.00 |
| 314_A | 318_N | 1.591 | 1.00 |
| 305_L | 383_Y | 1.585 | 1.00 |
| 249_A | 390_F | 1.582 | 1.00 |
| 169_G | 206_M | 1.581 | 1.00 |
| 340_E | 357_M | 1.579 | 1.00 |
| 233_Q | 236_E | 1.574 | 1.00 |
| 77_Q | 81_A | 1.569 | 1.00 |
| 362_F | 426_L | 1.568 | 1.00 |
| 91_V | 152_F | 1.556 | 1.00 |
| 304_K | 309_D | 1.539 | 1.00 |
| 358_Q | 422_K | 1.532 | 1.00 |
| 310_T | 314_A | 1.507 | 1.00 |
| 112_T | 134_H | 1.501 | 1.00 |
| 190_L | 197_V | 1.499 | 1.00 |
| 409_G | 424_F | 1.495 | 1.00 |
| 78_L | 83_R | 1.495 | 1.00 |
| 332_A | 336_V | 1.495 | 1.00 |
| 80_G | 306_G | 1.491 | 1.00 |
| 265_V | 424_F | 1.487 | 1.00 |
| 39_A | 195_C | 1.470 | 1.00 |
| 35_D | 199_T | 1.459 | 1.00 |
| 191_G | 194_G | 1.455 | 1.00 |
| 396_S | 435_A | 1.451 | 1.00 |
| 177_N | 195_C | 1.450 | 1.00 |
| 19_T | 23_I | 1.446 | 1.00 |
| 73_P | 77_Q | 1.437 | 1.00 |
| 122_E | 270_S | 1.436 | 1.00 |
| 193_V | 197_V | 1.436 | 1.00 |
| 98_A | 148_A | 1.436 | 1.00 |
| 44_A | 349_N | 1.428 | 1.00 |
| 301_V | 313_A | 1.421 | 1.00 |
| 269_G | 272_V | 1.409 | 1.00 |
| 264_L | 405_G | 1.409 | 1.00 |
| 341_Q | 344_L | 1.399 | 0.99 |
| 180_F | 190_L | 1.394 | 0.99 |
| 261_V | 405_G | 1.390 | 0.99 |
| 74_V | 243_L | 1.386 | 0.99 |
| 427_G | 431_G | 1.379 | 0.99 |
| 128_K | 131_G | 1.366 | 0.99 |
| 80_G | 307_E | 1.365 | 0.99 |
| 181_V | 195_C | 1.362 | 0.99 |
| 112_T | 130_V | 1.360 | 0.99 |
| 77_Q | 384_K | 1.359 | 0.99 |
| 264_L | 409_G | 1.356 | 0.99 |
| 391_H | 395_I | 1.352 | 0.99 |
| 176_L | 198_A | 1.352 | 0.99 |
| 419_L | 423_G | 1.351 | 0.99 |
| 178_W | 182_Y | 1.347 | 0.99 |
| 404_T | 427_G | 1.346 | 0.99 |
| 362_F | 429_I | 1.346 | 0.99 |
| 175_P | 179_I | 1.340 | 0.99 |
| 177_N | 198_A | 1.331 | 0.99 |
| 27_A | 167_F | 1.328 | 0.99 |
| 303_H | 307_E | 1.316 | 0.99 |
| 36_T | 281_N | 1.311 | 0.99 |
| 245_F | 249_A | 1.311 | 0.99 |
| 86_K | 89_F | 1.310 | 0.99 |
| 311_K | 315_I | 1.308 | 0.99 |
| 149_L | 210_L | 1.296 | 0.99 |
| 38_M | 177_N | 1.296 | 0.99 |
| 208_L | 212_F | 1.291 | 0.99 |
| 369_M | 436_A | 1.286 | 0.99 |
| 18_A | 296_A | 1.279 | 0.99 |
| 437_L | 441_Q | 1.278 | 0.99 |
| 350_Q | 354_A | 1.273 | 0.99 |
| 106_I | 141_P | 1.272 | 0.99 |
| 173_N | 199_T | 1.259 | 0.99 |
| 127_T | 131_G | 1.259 | 0.99 |
| 135_A | 197_V | 1.255 | 0.99 |
| 334_L | 338_F | 1.242 | 0.98 |
| 179_I | 184_K | 1.237 | 0.98 |
| 164_V | 168_I | 1.230 | 0.98 |
| 161_P | 213_Y | 1.226 | 0.98 |
| 328_A | 371_A | 1.214 | 0.98 |
| 114_F | 117_R | 1.214 | 0.98 |
| 100_L | 104_P | 1.213 | 0.98 |
| 40_G | 47_M | 1.211 | 0.98 |
| 176_L | 201_I | 1.209 | 0.98 |
| 126_A | 130_V | 1.205 | 0.98 |
| 135_A | 200_A | 1.201 | 0.98 |
| 265_V | 421_A | 1.201 | 0.98 |
| 326_A | 330_I | 1.179 | 0.98 |
| 74_V | 90_E | 1.178 | 0.98 |
| 53_A | 133_M | 1.175 | 0.98 |
| 399_V | 403_P | 1.175 | 0.98 |
| 322_M | 326_A | 1.168 | 0.97 |
| 45_I | 124_A | 1.166 | 0.97 |
| 400_L | 404_T | 1.166 | 0.97 |
| 392_R | 438_M | 1.160 | 0.97 |
| 405_G | 409_G | 1.154 | 0.97 |
| 78_L | 81_A | 1.149 | 0.97 |
| 279_A | 359_L | 1.149 | 0.97 |
| 113_Q | 134_H | 1.149 | 0.97 |
| 315_I | 318_N | 1.144 | 0.97 |
| 401_G | 431_G | 1.143 | 0.97 |
| 246_P | 386_M | 1.138 | 0.97 |
| 403_P | 407_I | 1.134 | 0.97 |
| 35_D | 177_N | 1.134 | 0.97 |
| 253_F | 394_F | 1.131 | 0.97 |
| 378_G | 382_G | 1.129 | 0.97 |
| 124_A | 127_T | 1.129 | 0.97 |
| 401_G | 428_F | 1.126 | 0.97 |
| 172_L | 176_L | 1.126 | 0.97 |
| 300_R | 316_A | 1.123 | 0.97 |
| 212_F | 216_T | 1.122 | 0.97 |
| 362_F | 422_K | 1.122 | 0.97 |
| 373_Q | 432_L | 1.118 | 0.96 |
| 379_S | 443_L | 1.117 | 0.96 |
| 324_G | 375_V | 1.109 | 0.96 |
| 172_L | 202_V | 1.105 | 0.96 |
| 312_G | 315_I | 1.104 | 0.96 |
| 93_Q | 237_L | 1.104 | 0.96 |
| 97_L | 237_L | 1.103 | 0.96 |
| 178_W | 181_V | 1.103 | 0.96 |
| 406_Y | 410_M | 1.102 | 0.96 |
| 77_Q | 239_R | 1.101 | 0.96 |
| 84_Q | 88_P | 1.099 | 0.96 |
| 173_N | 177_N | 1.097 | 0.96 |
| 351_V | 354_A | 1.096 | 0.96 |
| 123_E | 127_T | 1.092 | 0.96 |
| 176_L | 180_F | 1.088 | 0.96 |
| 37_I | 40_G | 1.084 | 0.96 |
| 401_G | 405_G | 1.082 | 0.96 |
| 235_K | 238_I | 1.082 | 0.96 |
| 341_Q | 345_L | 1.080 | 0.95 |
| 388_A | 442_R | 1.079 | 0.95 |
| 265_V | 276_H | 1.079 | 0.95 |
| 23_I | 163_M | 1.075 | 0.95 |
| 413_W | 418_P | 1.073 | 0.95 |
| 253_F | 390_F | 1.071 | 0.95 |
| 359_L | 421_A | 1.068 | 0.95 |
| 85_H | 89_F | 1.067 | 0.95 |
| 246_P | 390_F | 1.066 | 0.95 |
| 89_F | 93_Q | 1.065 | 0.95 |
| 76_A | 155_G | 1.063 | 0.95 |
| 50_V | 192_G | 1.060 | 0.95 |
| 171_L | 175_P | 1.059 | 0.95 |
| 407_I | 413_W | 1.056 | 0.95 |
| 24_A | 166_G | 1.054 | 0.95 |
| 324_G | 371_A | 1.051 | 0.94 |
| 239_R | 384_K | 1.050 | 0.94 |
| 252_F | 256_T | 1.050 | 0.94 |
| 232_P | 237_L | 1.049 | 0.94 |
| 353_V | 356_A | 1.045 | 0.94 |
| 408_L | 419_L | 1.040 | 0.94 |
| 180_F | 201_I | 1.039 | 0.94 |
| 110_F | 134_H | 1.038 | 0.94 |
| 395_I | 399_V | 1.032 | 0.94 |
| 408_L | 427_G | 1.030 | 0.94 |
| 380_L | 442_R | 1.029 | 0.94 |
| 158_L | 162_A | 1.028 | 0.94 |
| 78_L | 90_E | 1.026 | 0.94 |
| 133_M | 137_I | 1.025 | 0.93 |
| 292_S | 296_A | 1.022 | 0.93 |
| 179_I | 183_G | 1.021 | 0.93 |
| 261_V | 428_F | 1.020 | 0.93 |
| 441_Q | 445_W | 1.019 | 0.93 |
| 336_V | 364_A | 1.019 | 0.93 |
| 109_L | 134_H | 1.016 | 0.93 |
| 153_T | 214_I | 1.016 | 0.93 |
| 44_A | 274_A | 1.015 | 0.93 |
| 338_F | 342_I | 1.015 | 0.93 |
| 400_L | 403_P | 1.012 | 0.93 |
| 15_I | 19_T | 1.012 | 0.93 |
| 48_A | 274_A | 1.011 | 0.93 |
| 117_R | 126_A | 1.007 | 0.93 |
| 372_V | 436_A | 1.005 | 0.93 |
| 194_G | 198_A | 1.005 | 0.93 |
| 264_L | 406_Y | 1.005 | 0.93 |
| 138_F | 200_A | 1.003 | 0.93 |
| 392_R | 439_L | 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 | |
| 3mktA | 2 | 0.9848 | 100 | 0.172 | Contact Map |
| 4humA | 1 | 0.9891 | 100 | 0.208 | Contact Map |
| 3w4tA | 1 | 0.9478 | 100 | 0.244 | Contact Map |
| 4lz6A | 1 | 0.9543 | 100 | 0.249 | Contact Map |
| 4d2bA | 1 | 0.8065 | 86 | 0.923 | Contact Map |
| 1pw4A | 1 | 0.8478 | 82.7 | 0.926 | Contact Map |
| 4oh3A | 2 | 0.9087 | 74.3 | 0.932 | Contact Map |
| 4ikvA | 1 | 0.8652 | 62.7 | 0.937 | Contact Map |
| 4tphA | 2 | 0.8 | 51.7 | 0.941 | Contact Map |
| 4j05A | 2 | 0.8196 | 38.8 | 0.945 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)