| cypXXX |
| ID: | 1679406990 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 501 (471) | ||
| Sequences: | 17267 (11996.6) | ||
| Seq/Len: | 36.660 | ||
| Nf(neff/√len): | 552.8 |
HHblits Results: (2016_02)
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 |
| 362_A | 428_E | 4.934 | 1.00 |
| 418_D | 421_T | 4.262 | 1.00 |
| 336_N | 340_A | 3.822 | 1.00 |
| 418_D | 423_R | 3.779 | 1.00 |
| 320_L | 462_V | 3.747 | 1.00 |
| 332_Q | 336_N | 3.682 | 1.00 |
| 330_V | 359_Y | 3.508 | 1.00 |
| 323_H | 371_H | 3.425 | 1.00 |
| 333_K | 425_E | 3.216 | 1.00 |
| 268_R | 277_D | 3.172 | 1.00 |
| 387_G | 397_Q | 3.054 | 1.00 |
| 320_L | 367_T | 3.019 | 1.00 |
| 175_F | 321_L | 2.970 | 1.00 |
| 361_D | 459_A | 2.934 | 1.00 |
| 470_E | 496_R | 2.897 | 1.00 |
| 410_H | 420_D | 2.880 | 1.00 |
| 269_L | 295_R | 2.787 | 1.00 |
| 334_L | 363_V | 2.758 | 1.00 |
| 412_T | 419_A | 2.754 | 1.00 |
| 416_G | 419_A | 2.727 | 1.00 |
| 472_E | 494_G | 2.723 | 1.00 |
| 178_L | 461_I | 2.718 | 1.00 |
| 335_Q | 470_E | 2.692 | 1.00 |
| 61_H | 65_Q | 2.679 | 1.00 |
| 334_L | 466_F | 2.671 | 1.00 |
| 332_Q | 470_E | 2.569 | 1.00 |
| 266_N | 270_E | 2.534 | 1.00 |
| 333_K | 359_Y | 2.519 | 1.00 |
| 334_L | 360_V | 2.485 | 1.00 |
| 396_P | 399_T | 2.463 | 1.00 |
| 465_V | 471_F | 2.434 | 1.00 |
| 156_D | 468_R | 2.390 | 1.00 |
| 34_I | 78_V | 2.387 | 1.00 |
| 316_T | 458_L | 2.383 | 1.00 |
| 156_D | 469_Y | 2.380 | 1.00 |
| 389_T | 394_H | 2.313 | 1.00 |
| 335_Q | 498_R | 2.283 | 1.00 |
| 335_Q | 339_D | 2.278 | 1.00 |
| 364_I | 458_L | 2.257 | 1.00 |
| 339_D | 498_R | 2.249 | 1.00 |
| 320_L | 363_V | 2.237 | 1.00 |
| 266_N | 295_R | 2.216 | 1.00 |
| 175_F | 317_S | 2.185 | 1.00 |
| 387_G | 394_H | 2.166 | 1.00 |
| 363_V | 422_F | 2.161 | 1.00 |
| 331_V | 470_E | 2.161 | 1.00 |
| 70_L | 80_I | 2.153 | 1.00 |
| 149_Q | 464_T | 2.149 | 1.00 |
| 36_A | 67_L | 2.147 | 1.00 |
| 262_I | 266_N | 2.129 | 1.00 |
| 382_I | 395_F | 2.125 | 1.00 |
| 59_A | 62_E | 2.118 | 1.00 |
| 332_Q | 335_Q | 2.106 | 1.00 |
| 472_E | 496_R | 2.092 | 1.00 |
| 370_I | 410_H | 2.084 | 1.00 |
| 259_G | 263_A | 2.022 | 1.00 |
| 325_L | 331_V | 2.009 | 1.00 |
| 317_S | 461_I | 2.005 | 1.00 |
| 62_E | 65_Q | 1.995 | 1.00 |
| 324_C | 330_V | 1.984 | 1.00 |
| 359_Y | 425_E | 1.967 | 1.00 |
| 146_H | 185_D | 1.963 | 1.00 |
| 320_L | 324_C | 1.944 | 1.00 |
| 323_H | 327_H | 1.933 | 1.00 |
| 412_T | 417_P | 1.928 | 1.00 |
| 337_E | 357_L | 1.918 | 1.00 |
| 338_L | 463_A | 1.916 | 1.00 |
| 385_G | 397_Q | 1.886 | 1.00 |
| 389_T | 392_G | 1.880 | 1.00 |
| 86_I | 408_I | 1.866 | 1.00 |
| 124_K | 301_E | 1.859 | 1.00 |
| 316_T | 373_T | 1.843 | 1.00 |
| 384_P | 397_Q | 1.822 | 1.00 |
| 331_V | 335_Q | 1.819 | 1.00 |
| 412_T | 420_D | 1.809 | 1.00 |
| 406_Y | 410_H | 1.790 | 1.00 |
| 330_V | 363_V | 1.787 | 1.00 |
| 321_L | 465_V | 1.775 | 1.00 |
| 347_A | 353_Q | 1.772 | 1.00 |
| 150_E | 196_K | 1.761 | 1.00 |
| 148_L | 178_L | 1.734 | 1.00 |
| 471_F | 495_M | 1.718 | 1.00 |
| 137_V | 456_M | 1.689 | 1.00 |
| 350_S | 353_Q | 1.673 | 1.00 |
| 44_N | 47_L | 1.659 | 1.00 |
| 61_H | 407_T | 1.647 | 1.00 |
| 327_H | 330_V | 1.642 | 1.00 |
| 62_E | 66_K | 1.619 | 1.00 |
| 339_D | 467_R | 1.617 | 1.00 |
| 341_A | 357_L | 1.594 | 1.00 |
| 80_I | 89_V | 1.591 | 1.00 |
| 262_I | 299_T | 1.587 | 1.00 |
| 423_R | 429_K | 1.585 | 1.00 |
| 324_C | 331_V | 1.584 | 1.00 |
| 338_L | 357_L | 1.583 | 1.00 |
| 156_D | 497_K | 1.572 | 1.00 |
| 366_E | 369_R | 1.570 | 1.00 |
| 85_A | 391_L | 1.569 | 1.00 |
| 454_A | 458_L | 1.566 | 1.00 |
| 323_H | 370_I | 1.562 | 1.00 |
| 178_L | 182_V | 1.552 | 1.00 |
| 170_D | 173_N | 1.551 | 1.00 |
| 294_G | 297_E | 1.549 | 1.00 |
| 262_I | 295_R | 1.540 | 1.00 |
| 365_K | 438_F | 1.540 | 1.00 |
| 38_F | 41_A | 1.530 | 1.00 |
| 190_E | 267_A | 1.514 | 1.00 |
| 381_V | 398_G | 1.509 | 1.00 |
| 184_G | 192_F | 1.505 | 1.00 |
| 263_A | 267_A | 1.497 | 1.00 |
| 280_A | 284_E | 1.468 | 1.00 |
| 69_K | 82_D | 1.454 | 1.00 |
| 154_Q | 157_R | 1.450 | 1.00 |
| 71_V | 79_S | 1.445 | 1.00 |
| 361_D | 365_K | 1.440 | 1.00 |
| 322_Y | 326_Q | 1.434 | 1.00 |
| 193_G | 196_K | 1.433 | 1.00 |
| 65_Q | 412_T | 1.426 | 1.00 |
| 447_A | 451_R | 1.422 | 1.00 |
| 409_H | 440_P | 1.416 | 1.00 |
| 123_R | 297_E | 1.397 | 0.99 |
| 171_A | 321_L | 1.391 | 0.99 |
| 183_I | 187_A | 1.390 | 0.99 |
| 255_E | 259_G | 1.387 | 0.99 |
| 362_A | 425_E | 1.378 | 0.99 |
| 145_H | 464_T | 1.373 | 0.99 |
| 121_H | 125_R | 1.373 | 0.99 |
| 112_L | 449_V | 1.367 | 0.99 |
| 40_A | 46_W | 1.353 | 0.99 |
| 335_Q | 466_F | 1.352 | 0.99 |
| 119_A | 122_T | 1.336 | 0.99 |
| 317_S | 458_L | 1.329 | 0.99 |
| 147_N | 150_E | 1.327 | 0.99 |
| 323_H | 367_T | 1.324 | 0.99 |
| 95_G | 384_P | 1.324 | 0.99 |
| 267_A | 271_K | 1.321 | 0.99 |
| 40_A | 43_T | 1.320 | 0.99 |
| 264_R | 267_A | 1.319 | 0.99 |
| 266_N | 269_L | 1.307 | 0.99 |
| 147_N | 185_D | 1.306 | 0.99 |
| 321_L | 493_V | 1.304 | 0.99 |
| 78_V | 395_F | 1.301 | 0.99 |
| 368_M | 440_P | 1.298 | 0.99 |
| 464_T | 468_R | 1.295 | 0.99 |
| 320_L | 364_I | 1.282 | 0.99 |
| 324_C | 334_L | 1.280 | 0.99 |
| 321_L | 462_V | 1.278 | 0.99 |
| 180_F | 310_S | 1.265 | 0.99 |
| 409_H | 438_F | 1.264 | 0.99 |
| 325_L | 471_F | 1.245 | 0.98 |
| 186_L | 453_V | 1.243 | 0.98 |
| 59_A | 63_A | 1.242 | 0.98 |
| 81_A | 411_S | 1.241 | 0.98 |
| 382_I | 398_G | 1.241 | 0.98 |
| 316_T | 367_T | 1.239 | 0.98 |
| 179_A | 313_T | 1.235 | 0.98 |
| 152_Q | 464_T | 1.231 | 0.98 |
| 363_V | 367_T | 1.228 | 0.98 |
| 338_L | 360_V | 1.224 | 0.98 |
| 321_L | 466_F | 1.209 | 0.98 |
| 455_E | 459_A | 1.200 | 0.98 |
| 330_V | 423_R | 1.184 | 0.98 |
| 152_Q | 469_Y | 1.184 | 0.98 |
| 119_A | 123_R | 1.173 | 0.98 |
| 72_R | 76_N | 1.168 | 0.97 |
| 64_H | 79_S | 1.162 | 0.97 |
| 78_V | 399_T | 1.151 | 0.97 |
| 120_E | 123_R | 1.141 | 0.97 |
| 368_M | 438_F | 1.134 | 0.97 |
| 132_F | 449_V | 1.128 | 0.97 |
| 128_V | 449_V | 1.127 | 0.97 |
| 404_P | 407_T | 1.124 | 0.97 |
| 148_L | 460_L | 1.123 | 0.97 |
| 367_T | 422_F | 1.121 | 0.97 |
| 267_A | 270_E | 1.118 | 0.96 |
| 274_D | 284_E | 1.117 | 0.96 |
| 405_A | 439_I | 1.116 | 0.96 |
| 365_K | 455_E | 1.111 | 0.96 |
| 168_E | 474_R | 1.111 | 0.96 |
| 90_Y | 403_V | 1.106 | 0.96 |
| 328_P | 332_Q | 1.104 | 0.96 |
| 34_I | 393_R | 1.103 | 0.96 |
| 36_A | 44_N | 1.102 | 0.96 |
| 148_L | 152_Q | 1.100 | 0.96 |
| 154_Q | 158_R | 1.092 | 0.96 |
| 171_A | 493_V | 1.090 | 0.96 |
| 144_I | 456_M | 1.085 | 0.96 |
| 183_I | 309_G | 1.085 | 0.96 |
| 420_D | 423_R | 1.082 | 0.96 |
| 358_P | 362_A | 1.081 | 0.95 |
| 330_V | 425_E | 1.080 | 0.95 |
| 381_V | 400_V | 1.077 | 0.95 |
| 323_H | 326_Q | 1.076 | 0.95 |
| 151_L | 178_L | 1.071 | 0.95 |
| 86_I | 403_V | 1.070 | 0.95 |
| 80_I | 85_A | 1.068 | 0.95 |
| 268_R | 280_A | 1.067 | 0.95 |
| 333_K | 336_N | 1.063 | 0.95 |
| 329_E | 333_K | 1.062 | 0.95 |
| 286_R | 295_R | 1.060 | 0.95 |
| 154_Q | 174_W | 1.058 | 0.95 |
| 325_L | 473_L | 1.056 | 0.95 |
| 479_E | 489_L | 1.051 | 0.94 |
| 84_D | 87_T | 1.046 | 0.94 |
| 320_L | 422_F | 1.046 | 0.94 |
| 464_T | 467_R | 1.044 | 0.94 |
| 354_V | 459_A | 1.043 | 0.94 |
| 258_A | 296_E | 1.042 | 0.94 |
| 70_L | 393_R | 1.040 | 0.94 |
| 63_A | 71_V | 1.033 | 0.94 |
| 277_D | 280_A | 1.033 | 0.94 |
| 353_Q | 356_D | 1.033 | 0.94 |
| 153_N | 156_D | 1.031 | 0.94 |
| 293_L | 297_E | 1.030 | 0.94 |
| 394_H | 397_Q | 1.026 | 0.94 |
| 342_L | 467_R | 1.024 | 0.93 |
| 185_D | 191_P | 1.023 | 0.93 |
| 82_D | 85_A | 1.019 | 0.93 |
| 118_R | 121_H | 1.019 | 0.93 |
| 145_H | 149_Q | 1.017 | 0.93 |
| 329_E | 332_Q | 1.013 | 0.93 |
| 382_I | 397_Q | 1.012 | 0.93 |
| 233_P | 237_P | 1.012 | 0.93 |
| 69_K | 413_E | 1.007 | 0.93 |
| 360_V | 363_V | 1.003 | 0.93 |
| 147_N | 191_P | 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 | |
| 3n9yA | 2 | 0.8982 | 100 | 0.204 | Contact Map |
| 4r21A | 2 | 0.8184 | 100 | 0.209 | Contact Map |
| 2ij2A | 2 | 0.8743 | 100 | 0.213 | Contact Map |
| 3czhA | 2 | 0.8902 | 100 | 0.213 | Contact Map |
| 3k9vA | 2 | 0.8922 | 100 | 0.213 | Contact Map |
| 3nxuA | 2 | 0.8842 | 100 | 0.215 | Contact Map |
| 2hi4A | 1 | 0.8962 | 100 | 0.219 | Contact Map |
| 3tbgA | 4 | 0.8822 | 100 | 0.226 | Contact Map |
| 3pm0A | 1 | 0.8503 | 100 | 0.226 | Contact Map |
| 4lxjA | 1 | 0.9421 | 100 | 0.234 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)