| Yuan |
| ID: | 1483539512 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 586 (571) | ||
| Sequences: | 6915 (4459.7) | ||
| Seq/Len: | 12.110 | ||
| Nf(neff/√len): | 186.6 |
Jackhmmer Results: (2016_04)
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: 12.110).
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 |
| 234_Q | 251_K | 5.175 | 1.00 |
| 383_E | 387_R | 4.343 | 1.00 |
| 466_E | 470_K | 4.268 | 1.00 |
| 197_E | 522_A | 3.826 | 1.00 |
| 227_R | 283_N | 3.600 | 1.00 |
| 182_Q | 186_K | 3.510 | 1.00 |
| 80_M | 83_A | 3.244 | 1.00 |
| 443_A | 447_E | 3.176 | 1.00 |
| 358_L | 580_P | 3.061 | 1.00 |
| 216_E | 345_K | 3.049 | 1.00 |
| 458_Q | 462_N | 3.014 | 1.00 |
| 402_V | 411_M | 3.014 | 1.00 |
| 524_R | 528_E | 2.844 | 1.00 |
| 377_D | 569_R | 2.823 | 1.00 |
| 559_P | 563_E | 2.798 | 1.00 |
| 294_Q | 299_E | 2.673 | 1.00 |
| 358_L | 548_K | 2.646 | 1.00 |
| 207_T | 305_V | 2.622 | 1.00 |
| 176_R | 181_D | 2.560 | 1.00 |
| 81_F | 104_L | 2.469 | 1.00 |
| 246_V | 250_E | 2.464 | 1.00 |
| 476_L | 509_S | 2.457 | 1.00 |
| 68_L | 72_A | 2.433 | 1.00 |
| 220_Q | 223_A | 2.383 | 1.00 |
| 184_L | 189_Q | 2.356 | 1.00 |
| 524_R | 561_V | 2.351 | 1.00 |
| 108_A | 118_G | 2.257 | 1.00 |
| 220_Q | 286_H | 2.244 | 1.00 |
| 457_K | 461_E | 2.212 | 1.00 |
| 532_A | 550_E | 2.197 | 1.00 |
| 388_D | 573_K | 2.178 | 1.00 |
| 427_S | 430_G | 2.169 | 1.00 |
| 534_L | 544_L | 2.103 | 1.00 |
| 234_Q | 247_I | 2.081 | 1.00 |
| 214_G | 299_E | 2.079 | 1.00 |
| 528_E | 553_R | 2.069 | 1.00 |
| 357_W | 547_P | 2.058 | 1.00 |
| 229_Y | 235_E | 2.048 | 1.00 |
| 531_Q | 550_E | 2.015 | 1.00 |
| 222_R | 225_E | 2.013 | 1.00 |
| 560_E | 564_Q | 2.011 | 1.00 |
| 317_N | 329_A | 2.009 | 1.00 |
| 181_D | 185_T | 2.000 | 1.00 |
| 306_R | 309_T | 1.998 | 1.00 |
| 556_E | 560_E | 1.984 | 1.00 |
| 221_L | 291_G | 1.982 | 1.00 |
| 61_A | 64_D | 1.958 | 1.00 |
| 102_F | 107_A | 1.952 | 1.00 |
| 462_N | 466_E | 1.948 | 1.00 |
| 356_D | 548_K | 1.946 | 1.00 |
| 78_K | 99_G | 1.930 | 1.00 |
| 282_E | 286_H | 1.925 | 1.00 |
| 33_M | 41_P | 1.918 | 1.00 |
| 360_F | 546_A | 1.907 | 1.00 |
| 403_S | 406_E | 1.900 | 1.00 |
| 551_I | 578_Y | 1.899 | 1.00 |
| 377_D | 382_I | 1.897 | 1.00 |
| 532_A | 554_L | 1.887 | 1.00 |
| 232_A | 280_I | 1.875 | 1.00 |
| 228_I | 238_I | 1.873 | 1.00 |
| 544_L | 554_L | 1.855 | 1.00 |
| 522_A | 526_K | 1.844 | 1.00 |
| 174_D | 177_N | 1.844 | 1.00 |
| 197_E | 526_K | 1.834 | 1.00 |
| 209_R | 348_Q | 1.820 | 1.00 |
| 91_K | 200_F | 1.801 | 1.00 |
| 119_D | 122_A | 1.800 | 1.00 |
| 50_E | 53_R | 1.799 | 1.00 |
| 187_L | 477_L | 1.790 | 1.00 |
| 455_G | 458_Q | 1.790 | 1.00 |
| 234_Q | 246_V | 1.787 | 1.00 |
| 516_K | 565_A | 1.786 | 1.00 |
| 210_L | 349_A | 1.758 | 1.00 |
| 201_T | 533_R | 1.752 | 1.00 |
| 444_E | 448_R | 1.745 | 1.00 |
| 231_L | 283_N | 1.742 | 1.00 |
| 524_R | 527_E | 1.740 | 1.00 |
| 544_L | 558_V | 1.733 | 1.00 |
| 389_L | 394_K | 1.733 | 1.00 |
| 194_I | 519_I | 1.730 | 1.00 |
| 209_R | 212_Q | 1.729 | 1.00 |
| 516_K | 520_D | 1.728 | 1.00 |
| 520_D | 523_A | 1.721 | 1.00 |
| 520_D | 561_V | 1.715 | 1.00 |
| 393_T | 404_E | 1.710 | 1.00 |
| 246_V | 251_K | 1.705 | 1.00 |
| 379_D | 455_G | 1.685 | 1.00 |
| 102_F | 184_L | 1.673 | 1.00 |
| 438_T | 441_E | 1.654 | 1.00 |
| 551_I | 555_C | 1.649 | 1.00 |
| 275_A | 282_E | 1.649 | 1.00 |
| 547_P | 550_E | 1.648 | 1.00 |
| 475_T | 508_G | 1.639 | 1.00 |
| 472_Y | 480_R | 1.634 | 1.00 |
| 395_T | 419_N | 1.634 | 1.00 |
| 465_Q | 469_Q | 1.631 | 1.00 |
| 203_V | 535_L | 1.630 | 1.00 |
| 204_N | 353_S | 1.625 | 1.00 |
| 170_P | 174_D | 1.622 | 1.00 |
| 382_I | 386_Q | 1.621 | 1.00 |
| 477_L | 566_V | 1.615 | 1.00 |
| 226_Q | 235_E | 1.595 | 1.00 |
| 74_E | 98_R | 1.590 | 1.00 |
| 206_D | 351_V | 1.590 | 1.00 |
| 372_L | 423_V | 1.587 | 1.00 |
| 557_L | 561_V | 1.583 | 1.00 |
| 204_N | 351_V | 1.572 | 1.00 |
| 524_R | 560_E | 1.571 | 1.00 |
| 218_A | 294_Q | 1.568 | 1.00 |
| 531_Q | 547_P | 1.564 | 1.00 |
| 73_D | 76_K | 1.557 | 1.00 |
| 229_Y | 238_I | 1.555 | 1.00 |
| 474_T | 480_R | 1.554 | 1.00 |
| 414_Q | 441_E | 1.547 | 1.00 |
| 525_L | 554_L | 1.528 | 1.00 |
| 213_M | 217_L | 1.526 | 1.00 |
| 421_G | 426_I | 1.525 | 1.00 |
| 267_S | 270_V | 1.523 | 1.00 |
| 220_Q | 342_E | 1.522 | 1.00 |
| 65_S | 68_L | 1.521 | 1.00 |
| 580_P | 584_D | 1.514 | 1.00 |
| 524_R | 557_L | 1.514 | 1.00 |
| 428_D | 443_A | 1.507 | 1.00 |
| 252_L | 278_H | 1.497 | 1.00 |
| 239_N | 287_Y | 1.492 | 1.00 |
| 135_D | 139_Y | 1.481 | 1.00 |
| 552_E | 555_C | 1.480 | 1.00 |
| 491_F | 495_S | 1.478 | 1.00 |
| 211_E | 302_L | 1.477 | 1.00 |
| 168_E | 172_M | 1.462 | 1.00 |
| 156_H | 160_K | 1.461 | 1.00 |
| 82_D | 85_R | 1.459 | 1.00 |
| 546_A | 554_L | 1.454 | 1.00 |
| 555_C | 559_P | 1.439 | 1.00 |
| 88_V | 196_A | 1.437 | 1.00 |
| 392_H | 420_F | 1.434 | 1.00 |
| 371_V | 506_I | 1.432 | 1.00 |
| 468_K | 498_E | 1.432 | 1.00 |
| 314_T | 328_S | 1.424 | 1.00 |
| 554_L | 558_V | 1.418 | 1.00 |
| 223_A | 227_R | 1.418 | 1.00 |
| 461_E | 464_V | 1.417 | 1.00 |
| 227_R | 230_E | 1.411 | 1.00 |
| 523_A | 527_E | 1.400 | 0.99 |
| 60_T | 64_D | 1.399 | 0.99 |
| 316_F | 536_L | 1.397 | 0.99 |
| 226_Q | 230_E | 1.387 | 0.99 |
| 397_M | 403_S | 1.387 | 0.99 |
| 72_A | 95_I | 1.385 | 0.99 |
| 360_F | 551_I | 1.382 | 0.99 |
| 345_K | 348_Q | 1.380 | 0.99 |
| 115_Q | 126_M | 1.374 | 0.99 |
| 521_L | 561_V | 1.373 | 0.99 |
| 379_D | 383_E | 1.367 | 0.99 |
| 353_S | 357_W | 1.360 | 0.99 |
| 374_H | 569_R | 1.359 | 0.99 |
| 398_D | 452_S | 1.357 | 0.99 |
| 410_N | 414_Q | 1.346 | 0.99 |
| 187_L | 516_K | 1.344 | 0.99 |
| 357_W | 545_E | 1.344 | 0.99 |
| 485_D | 497_A | 1.341 | 0.99 |
| 218_A | 222_R | 1.340 | 0.99 |
| 448_R | 451_A | 1.335 | 0.99 |
| 348_Q | 583_Y | 1.332 | 0.99 |
| 362_A | 576_Y | 1.331 | 0.99 |
| 311_K | 353_S | 1.323 | 0.99 |
| 162_A | 166_A | 1.322 | 0.99 |
| 36_N | 39_D | 1.321 | 0.99 |
| 496_F | 500_T | 1.316 | 0.99 |
| 209_R | 349_A | 1.316 | 0.99 |
| 495_S | 498_E | 1.315 | 0.99 |
| 447_E | 451_A | 1.312 | 0.99 |
| 276_P | 282_E | 1.306 | 0.99 |
| 47_L | 57_R | 1.306 | 0.99 |
| 77_K | 101_A | 1.303 | 0.99 |
| 124_A | 163_A | 1.301 | 0.99 |
| 25_K | 79_S | 1.300 | 0.99 |
| 173_D | 177_N | 1.300 | 0.99 |
| 465_Q | 468_K | 1.291 | 0.99 |
| 374_H | 568_L | 1.287 | 0.99 |
| 382_I | 569_R | 1.283 | 0.99 |
| 240_S | 243_Q | 1.280 | 0.99 |
| 34_E | 40_A | 1.279 | 0.99 |
| 207_T | 211_E | 1.277 | 0.99 |
| 417_A | 434_N | 1.270 | 0.99 |
| 247_I | 251_K | 1.265 | 0.99 |
| 217_L | 298_I | 1.263 | 0.99 |
| 214_G | 298_I | 1.247 | 0.99 |
| 491_F | 494_R | 1.242 | 0.98 |
| 513_I | 572_L | 1.240 | 0.98 |
| 358_L | 578_Y | 1.238 | 0.98 |
| 532_A | 547_P | 1.236 | 0.98 |
| 408_T | 411_M | 1.231 | 0.98 |
| 530_L | 553_R | 1.231 | 0.98 |
| 531_Q | 549_E | 1.230 | 0.98 |
| 483_L | 497_A | 1.221 | 0.98 |
| 172_M | 176_R | 1.213 | 0.98 |
| 548_K | 580_P | 1.212 | 0.98 |
| 559_P | 576_Y | 1.211 | 0.98 |
| 183_L | 187_L | 1.208 | 0.98 |
| 581_T | 584_D | 1.203 | 0.98 |
| 208_K | 212_Q | 1.201 | 0.98 |
| 486_I | 497_A | 1.200 | 0.98 |
| 563_E | 573_K | 1.200 | 0.98 |
| 521_L | 544_L | 1.198 | 0.98 |
| 383_E | 386_Q | 1.196 | 0.98 |
| 550_E | 553_R | 1.195 | 0.98 |
| 352_P | 359_I | 1.194 | 0.98 |
| 82_D | 105_L | 1.193 | 0.98 |
| 229_Y | 236_F | 1.192 | 0.98 |
| 460_M | 502_M | 1.191 | 0.98 |
| 125_K | 131_A | 1.182 | 0.98 |
| 91_K | 197_E | 1.179 | 0.98 |
| 530_L | 550_E | 1.178 | 0.98 |
| 555_C | 578_Y | 1.177 | 0.98 |
| 87_V | 196_A | 1.171 | 0.98 |
| 106_L | 192_A | 1.163 | 0.97 |
| 224_I | 283_N | 1.162 | 0.97 |
| 106_L | 319_A | 1.161 | 0.97 |
| 79_S | 168_E | 1.160 | 0.97 |
| 393_T | 409_A | 1.158 | 0.97 |
| 439_R | 443_A | 1.153 | 0.97 |
| 70_W | 76_K | 1.153 | 0.97 |
| 441_E | 444_E | 1.149 | 0.97 |
| 201_T | 522_A | 1.145 | 0.97 |
| 389_L | 404_E | 1.141 | 0.97 |
| 428_D | 439_R | 1.136 | 0.97 |
| 73_D | 78_K | 1.131 | 0.97 |
| 174_D | 178_N | 1.122 | 0.97 |
| 237_N | 240_S | 1.120 | 0.96 |
| 378_D | 455_G | 1.120 | 0.96 |
| 83_A | 192_A | 1.120 | 0.96 |
| 317_N | 327_S | 1.116 | 0.96 |
| 380_N | 383_E | 1.115 | 0.96 |
| 360_F | 555_C | 1.113 | 0.96 |
| 88_V | 200_F | 1.111 | 0.96 |
| 479_R | 512_D | 1.110 | 0.96 |
| 552_E | 556_E | 1.106 | 0.96 |
| 513_I | 566_V | 1.106 | 0.96 |
| 353_S | 545_E | 1.103 | 0.96 |
| 41_P | 93_K | 1.098 | 0.96 |
| 232_A | 236_F | 1.098 | 0.96 |
| 225_E | 229_Y | 1.094 | 0.96 |
| 30_V | 42_I | 1.094 | 0.96 |
| 237_N | 243_Q | 1.089 | 0.96 |
| 275_A | 281_V | 1.087 | 0.96 |
| 109_Y | 320_L | 1.086 | 0.96 |
| 358_L | 551_I | 1.085 | 0.96 |
| 276_P | 281_V | 1.085 | 0.96 |
| 268_A | 285_L | 1.082 | 0.96 |
| 268_A | 272_E | 1.075 | 0.95 |
| 394_K | 398_D | 1.072 | 0.95 |
| 160_K | 164_I | 1.072 | 0.95 |
| 278_H | 281_V | 1.068 | 0.95 |
| 242_K | 246_V | 1.068 | 0.95 |
| 82_D | 86_A | 1.067 | 0.95 |
| 112_N | 115_Q | 1.063 | 0.95 |
| 172_M | 185_T | 1.062 | 0.95 |
| 450_F | 457_K | 1.061 | 0.95 |
| 357_W | 533_R | 1.058 | 0.95 |
| 204_N | 354_E | 1.058 | 0.95 |
| 557_L | 560_E | 1.057 | 0.95 |
| 564_Q | 567_T | 1.056 | 0.95 |
| 468_K | 494_R | 1.054 | 0.95 |
| 227_R | 231_L | 1.052 | 0.95 |
| 485_D | 493_V | 1.047 | 0.94 |
| 518_M | 542_L | 1.047 | 0.94 |
| 261_K | 264_Y | 1.047 | 0.94 |
| 211_E | 215_S | 1.043 | 0.94 |
| 28_L | 90_L | 1.042 | 0.94 |
| 17_I | 20_E | 1.035 | 0.94 |
| 461_E | 465_Q | 1.034 | 0.94 |
| 136_E | 141_K | 1.028 | 0.94 |
| 134_S | 137_A | 1.027 | 0.94 |
| 236_F | 247_I | 1.026 | 0.94 |
| 219_E | 223_A | 1.024 | 0.93 |
| 204_N | 352_P | 1.021 | 0.93 |
| 375_I | 506_I | 1.020 | 0.93 |
| 577_H | 585_A | 1.017 | 0.93 |
| 28_L | 45_I | 1.016 | 0.93 |
| 418_V | 445_F | 1.016 | 0.93 |
| 222_R | 226_Q | 1.013 | 0.93 |
| 362_A | 558_V | 1.011 | 0.93 |
| 68_L | 95_I | 1.009 | 0.93 |
| 407_V | 411_M | 1.008 | 0.93 |
| 120_I | 164_I | 1.007 | 0.93 |
| 402_V | 407_V | 1.005 | 0.93 |
| 279_E | 282_E | 1.004 | 0.93 |
| 228_I | 280_I | 1.003 | 0.93 |
| 60_T | 63_A | 1.003 | 0.93 |
| 215_S | 218_A | 1.003 | 0.93 |
| 430_G | 434_N | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2kfnA | 1 | 0.9932 | 100 | 0.077 | Contact Map |
| 4yfuA | 2 | 0 | 100 | 0.089 | Contact Map |
| 4bwjA | 1 | 0.913 | 100 | 0.118 | Contact Map |
| 4x0qA | 2 | 0.9266 | 100 | 0.136 | Contact Map |
| 4xvkA | 1 | 0.942 | 100 | 0.155 | Contact Map |
| 1bgxT | 1 | 0.9283 | 100 | 0.159 | Contact Map |
| 1x9mA | 1 | 0.9198 | 100 | 0.189 | Contact Map |
| 3ikmA | 2 | 0.9249 | 100 | 0.544 | Contact Map |
| 1yt3A | 1 | 0.587 | 100 | 0.776 | Contact Map |
| 2e6mA | 1 | 0.2901 | 99.9 | 0.852 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)