| lntPae |
| ID: | 1488186403 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 511 (476) | ||
| Sequences: | 2001 (1322.1) | ||
| Seq/Len: | 4.204 | ||
| Nf(neff/√len): | 60.6 |
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: 4.204).
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 |
| 166_G | 170_L | 6.416 | 1.00 |
| 447_D | 451_R | 5.277 | 1.00 |
| 456_I | 462_G | 4.412 | 1.00 |
| 420_L | 444_G | 4.133 | 1.00 |
| 232_G | 252_Y | 3.750 | 1.00 |
| 430_S | 478_L | 3.669 | 1.00 |
| 318_I | 404_V | 3.597 | 1.00 |
| 55_L | 104_A | 3.528 | 1.00 |
| 160_A | 428_L | 3.409 | 1.00 |
| 405_S | 438_T | 3.168 | 1.00 |
| 477_Y | 482_V | 3.085 | 1.00 |
| 426_R | 429_E | 2.989 | 1.00 |
| 154_Q | 175_I | 2.812 | 1.00 |
| 256_S | 267_W | 2.789 | 1.00 |
| 124_A | 128_A | 2.781 | 1.00 |
| 229_A | 443_T | 2.754 | 1.00 |
| 317_G | 329_L | 2.724 | 1.00 |
| 377_I | 400_V | 2.557 | 1.00 |
| 228_V | 262_V | 2.537 | 1.00 |
| 427_A | 434_M | 2.491 | 1.00 |
| 401_L | 434_M | 2.370 | 1.00 |
| 23_P | 68_A | 2.362 | 1.00 |
| 69_G | 148_L | 2.301 | 1.00 |
| 59_W | 97_A | 2.292 | 1.00 |
| 420_L | 452_I | 2.283 | 1.00 |
| 343_Q | 359_D | 2.262 | 1.00 |
| 251_L | 461_Q | 2.222 | 1.00 |
| 152_Y | 425_M | 2.219 | 1.00 |
| 256_S | 265_I | 2.217 | 1.00 |
| 151_G | 168_V | 2.188 | 1.00 |
| 16_L | 60_W | 2.177 | 1.00 |
| 228_V | 465_R | 2.148 | 1.00 |
| 22_T | 40_A | 2.108 | 1.00 |
| 420_L | 446_I | 2.086 | 1.00 |
| 163_V | 425_M | 2.052 | 1.00 |
| 76_S | 410_F | 2.045 | 1.00 |
| 110_W | 127_F | 2.026 | 1.00 |
| 476_P | 480_Y | 1.999 | 1.00 |
| 132_L | 173_F | 1.988 | 1.00 |
| 229_A | 437_A | 1.982 | 1.00 |
| 443_T | 456_I | 1.981 | 1.00 |
| 392_A | 481_R | 1.971 | 1.00 |
| 433_W | 448_P | 1.963 | 1.00 |
| 227_V | 435_I | 1.956 | 1.00 |
| 302_P | 360_F | 1.947 | 1.00 |
| 290_A | 297_L | 1.930 | 1.00 |
| 434_M | 446_I | 1.929 | 1.00 |
| 303_V | 329_L | 1.921 | 1.00 |
| 164_P | 431_G | 1.899 | 1.00 |
| 12_H | 60_W | 1.848 | 1.00 |
| 163_V | 171_S | 1.837 | 1.00 |
| 58_G | 104_A | 1.820 | 1.00 |
| 15_A | 57_R | 1.815 | 1.00 |
| 318_I | 379_P | 1.811 | 1.00 |
| 385_V | 434_M | 1.801 | 1.00 |
| 417_L | 442_V | 1.785 | 1.00 |
| 431_G | 475_T | 1.784 | 1.00 |
| 380_Y | 391_A | 1.763 | 0.99 |
| 136_L | 140_W | 1.743 | 0.99 |
| 63_F | 100_A | 1.722 | 0.99 |
| 301_V | 319_T | 1.718 | 0.99 |
| 407_D | 419_H | 1.707 | 0.99 |
| 128_A | 177_L | 1.678 | 0.99 |
| 298_I | 320_V | 1.662 | 0.99 |
| 15_A | 46_L | 1.634 | 0.99 |
| 250_D | 254_D | 1.628 | 0.99 |
| 228_V | 463_I | 1.626 | 0.99 |
| 40_A | 61_Y | 1.618 | 0.99 |
| 252_Y | 271_A | 1.606 | 0.99 |
| 298_I | 402_L | 1.596 | 0.99 |
| 63_F | 67_G | 1.595 | 0.99 |
| 58_G | 62_G | 1.580 | 0.99 |
| 262_V | 465_R | 1.578 | 0.99 |
| 375_Y | 399_Q | 1.578 | 0.99 |
| 164_P | 208_A | 1.552 | 0.98 |
| 385_V | 403_T | 1.531 | 0.98 |
| 407_D | 436_R | 1.530 | 0.98 |
| 42_L | 127_F | 1.522 | 0.98 |
| 152_Y | 422_M | 1.515 | 0.98 |
| 164_P | 428_L | 1.498 | 0.98 |
| 238_L | 244_Q | 1.497 | 0.98 |
| 485_L | 489_A | 1.493 | 0.98 |
| 233_N | 461_Q | 1.484 | 0.98 |
| 332_K | 390_F | 1.468 | 0.97 |
| 161_G | 209_G | 1.465 | 0.97 |
| 433_W | 468_V | 1.464 | 0.97 |
| 446_I | 452_I | 1.464 | 0.97 |
| 378_A | 401_L | 1.454 | 0.97 |
| 423_A | 434_M | 1.454 | 0.97 |
| 70_T | 145_F | 1.450 | 0.97 |
| 154_Q | 171_S | 1.447 | 0.97 |
| 229_A | 464_L | 1.420 | 0.97 |
| 60_W | 64_G | 1.406 | 0.96 |
| 376_Q | 399_Q | 1.398 | 0.96 |
| 380_Y | 385_V | 1.397 | 0.96 |
| 73_I | 271_A | 1.393 | 0.96 |
| 73_I | 92_M | 1.392 | 0.96 |
| 424_Q | 452_I | 1.378 | 0.96 |
| 46_L | 107_A | 1.376 | 0.96 |
| 156_Q | 424_Q | 1.376 | 0.96 |
| 149_Y | 152_Y | 1.369 | 0.96 |
| 371_K | 376_Q | 1.359 | 0.95 |
| 246_R | 250_D | 1.357 | 0.95 |
| 22_T | 61_Y | 1.351 | 0.95 |
| 132_L | 172_S | 1.345 | 0.95 |
| 15_A | 19_G | 1.338 | 0.95 |
| 236_Q | 239_K | 1.336 | 0.95 |
| 66_F | 138_R | 1.330 | 0.95 |
| 20_A | 68_A | 1.326 | 0.95 |
| 399_Q | 470_P | 1.313 | 0.94 |
| 165_V | 208_A | 1.309 | 0.94 |
| 266_V | 435_I | 1.302 | 0.94 |
| 264_L | 298_I | 1.294 | 0.94 |
| 239_K | 270_T | 1.284 | 0.93 |
| 162_L | 209_G | 1.284 | 0.93 |
| 435_I | 443_T | 1.280 | 0.93 |
| 454_R | 464_L | 1.277 | 0.93 |
| 400_V | 468_V | 1.273 | 0.93 |
| 233_N | 440_N | 1.272 | 0.93 |
| 270_T | 302_P | 1.270 | 0.93 |
| 400_V | 435_I | 1.251 | 0.92 |
| 22_T | 25_A | 1.243 | 0.92 |
| 317_G | 327_T | 1.233 | 0.91 |
| 229_A | 435_I | 1.232 | 0.91 |
| 204_G | 207_A | 1.229 | 0.91 |
| 420_L | 434_M | 1.215 | 0.90 |
| 417_L | 458_Q | 1.213 | 0.90 |
| 227_V | 445_L | 1.211 | 0.90 |
| 43_Y | 183_V | 1.209 | 0.90 |
| 171_S | 174_V | 1.208 | 0.90 |
| 19_G | 64_G | 1.207 | 0.90 |
| 52_K | 56_W | 1.200 | 0.90 |
| 137_F | 141_F | 1.199 | 0.90 |
| 272_V | 301_V | 1.187 | 0.89 |
| 435_I | 445_L | 1.186 | 0.89 |
| 54_A | 111_A | 1.185 | 0.89 |
| 201_L | 205_P | 1.180 | 0.89 |
| 138_R | 144_G | 1.177 | 0.88 |
| 71_S | 414_I | 1.177 | 0.88 |
| 303_V | 317_G | 1.172 | 0.88 |
| 448_P | 471_M | 1.168 | 0.88 |
| 270_T | 439_N | 1.167 | 0.88 |
| 277_D | 304_R | 1.163 | 0.88 |
| 474_L | 479_Q | 1.156 | 0.87 |
| 401_L | 430_S | 1.155 | 0.87 |
| 266_V | 402_L | 1.153 | 0.87 |
| 11_G | 57_R | 1.146 | 0.87 |
| 419_H | 436_R | 1.143 | 0.86 |
| 171_S | 425_M | 1.142 | 0.86 |
| 51_G | 108_W | 1.142 | 0.86 |
| 161_G | 164_P | 1.141 | 0.86 |
| 416_P | 458_Q | 1.141 | 0.86 |
| 389_E | 482_V | 1.139 | 0.86 |
| 433_W | 469_I | 1.138 | 0.86 |
| 248_Q | 273_P | 1.135 | 0.86 |
| 85_V | 89_S | 1.134 | 0.86 |
| 75_V | 413_S | 1.133 | 0.86 |
| 264_L | 402_L | 1.133 | 0.86 |
| 139_S | 169_W | 1.124 | 0.85 |
| 227_V | 266_V | 1.121 | 0.85 |
| 22_T | 150_A | 1.121 | 0.85 |
| 275_L | 302_P | 1.118 | 0.85 |
| 161_G | 428_L | 1.113 | 0.84 |
| 87_L | 90_L | 1.106 | 0.84 |
| 316_N | 409_W | 1.090 | 0.83 |
| 320_V | 370_L | 1.090 | 0.83 |
| 181_L | 198_G | 1.088 | 0.83 |
| 264_L | 400_V | 1.088 | 0.83 |
| 129_A | 489_A | 1.085 | 0.82 |
| 239_K | 271_A | 1.082 | 0.82 |
| 101_F | 105_L | 1.081 | 0.82 |
| 165_V | 476_P | 1.079 | 0.82 |
| 160_A | 164_P | 1.076 | 0.82 |
| 404_V | 437_A | 1.075 | 0.81 |
| 296_A | 320_V | 1.071 | 0.81 |
| 24_L | 29_F | 1.070 | 0.81 |
| 287_G | 291_D | 1.069 | 0.81 |
| 407_D | 415_G | 1.065 | 0.81 |
| 149_Y | 172_S | 1.064 | 0.81 |
| 98_G | 103_F | 1.060 | 0.80 |
| 137_F | 140_W | 1.059 | 0.80 |
| 123_D | 128_A | 1.056 | 0.80 |
| 406_N | 436_R | 1.055 | 0.80 |
| 419_H | 423_A | 1.052 | 0.80 |
| 106_P | 130_L | 1.051 | 0.79 |
| 54_A | 58_G | 1.049 | 0.79 |
| 178_S | 206_W | 1.045 | 0.79 |
| 407_D | 416_P | 1.042 | 0.79 |
| 378_A | 398_S | 1.038 | 0.78 |
| 135_E | 172_S | 1.034 | 0.78 |
| 71_S | 413_S | 1.034 | 0.78 |
| 29_F | 414_I | 1.032 | 0.78 |
| 244_Q | 248_Q | 1.031 | 0.78 |
| 63_F | 97_A | 1.030 | 0.77 |
| 255_L | 258_P | 1.022 | 0.77 |
| 230_I | 463_I | 1.018 | 0.76 |
| 435_I | 468_V | 1.017 | 0.76 |
| 305_E | 487_G | 1.009 | 0.75 |
| 16_L | 64_G | 1.009 | 0.75 |
| 71_S | 75_V | 1.008 | 0.75 |
| 377_I | 402_L | 1.006 | 0.75 |
| 433_W | 445_L | 1.003 | 0.75 |
| 230_I | 265_I | 1.003 | 0.75 |
| 265_I | 295_A | 1.001 | 0.75 |
| 98_G | 102_F | 1.001 | 0.75 |
| 315_F | 329_L | 1.000 | 0.75 |
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 | |
| 1uf5A | 2 | 0.5049 | 100 | 0.7 | Contact Map |
| 2w1vA | 2 | 0.4795 | 100 | 0.729 | Contact Map |
| 3p8kA | 2 | 0.4736 | 100 | 0.73 | Contact Map |
| 1f89A | 2 | 0.4697 | 100 | 0.731 | Contact Map |
| 3ivzA | 2 | 0.454 | 100 | 0.734 | Contact Map |
| 2e11A | 4 | 0.4599 | 100 | 0.734 | Contact Map |
| 2dyuA | 2 | 0.4951 | 100 | 0.737 | Contact Map |
| 4f4hA | 2 | 0.5127 | 100 | 0.738 | Contact Map |
| 4lf0A | 1 | 0.5068 | 100 | 0.739 | Contact Map |
| 4izuA | 1 | 0.4423 | 100 | 0.739 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)