| test |
| ID: | 1382752092 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 671 (590) | ||
| Sequences: | 1789 (1091.5) | ||
| Seq/Len: | 3.032 | ||
| Nf(neff/√len): | 44.9 |
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: 3.032).
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 |
| 137_Y | 184_E | 5.441 | 1.00 |
| 141_K | 160_H | 4.570 | 1.00 |
| 383_R | 416_D | 4.179 | 1.00 |
| 352_A | 519_I | 3.902 | 1.00 |
| 28_Q | 73_K | 3.860 | 1.00 |
| 308_R | 316_E | 3.679 | 1.00 |
| 387_M | 397_C | 3.617 | 1.00 |
| 447_G | 460_T | 3.610 | 1.00 |
| 295_D | 320_R | 3.460 | 1.00 |
| 476_S | 479_A | 3.380 | 1.00 |
| 68_K | 660_F | 3.340 | 1.00 |
| 436_Q | 459_Q | 3.247 | 1.00 |
| 178_T | 203_C | 3.077 | 1.00 |
| 173_D | 176_E | 2.982 | 1.00 |
| 350_D | 354_N | 2.927 | 1.00 |
| 154_I | 185_L | 2.881 | 1.00 |
| 23_L | 92_G | 2.855 | 1.00 |
| 352_A | 485_I | 2.852 | 1.00 |
| 204_D | 274_L | 2.652 | 1.00 |
| 521_Q | 611_E | 2.637 | 1.00 |
| 520_K | 524_K | 2.628 | 1.00 |
| 143_H | 160_H | 2.615 | 1.00 |
| 204_D | 297_A | 2.605 | 1.00 |
| 247_P | 297_A | 2.599 | 1.00 |
| 158_F | 181_V | 2.584 | 1.00 |
| 198_Y | 201_E | 2.582 | 1.00 |
| 526_E | 649_W | 2.553 | 1.00 |
| 65_T | 75_K | 2.542 | 1.00 |
| 143_H | 159_K | 2.491 | 1.00 |
| 107_E | 148_E | 2.490 | 1.00 |
| 122_V | 151_T | 2.312 | 1.00 |
| 355_T | 466_I | 2.297 | 1.00 |
| 421_F | 435_L | 2.246 | 1.00 |
| 287_K | 324_T | 2.234 | 1.00 |
| 422_V | 487_L | 2.210 | 1.00 |
| 201_E | 298_H | 2.142 | 1.00 |
| 305_R | 317_S | 2.127 | 1.00 |
| 119_E | 197_H | 2.116 | 1.00 |
| 383_R | 414_F | 2.106 | 1.00 |
| 192_L | 202_V | 2.098 | 1.00 |
| 158_F | 193_V | 2.086 | 1.00 |
| 404_F | 491_A | 2.079 | 1.00 |
| 504_R | 507_E | 2.058 | 1.00 |
| 519_I | 641_I | 2.032 | 1.00 |
| 175_N | 307_H | 2.020 | 1.00 |
| 135_R | 139_L | 2.018 | 1.00 |
| 397_C | 422_V | 2.012 | 1.00 |
| 480_Y | 554_T | 2.010 | 1.00 |
| 161_F | 184_E | 1.998 | 1.00 |
| 404_F | 494_L | 1.991 | 1.00 |
| 154_I | 191_L | 1.990 | 1.00 |
| 263_E | 289_L | 1.979 | 1.00 |
| 158_F | 178_T | 1.963 | 1.00 |
| 25_E | 283_Q | 1.954 | 1.00 |
| 17_G | 271_E | 1.951 | 1.00 |
| 24_I | 40_I | 1.936 | 0.99 |
| 538_N | 653_N | 1.930 | 0.99 |
| 122_V | 155_A | 1.915 | 0.99 |
| 65_T | 106_T | 1.907 | 0.99 |
| 382_C | 418_T | 1.906 | 0.99 |
| 521_Q | 524_K | 1.904 | 0.99 |
| 559_A | 570_S | 1.893 | 0.99 |
| 70_K | 74_Q | 1.893 | 0.99 |
| 346_F | 526_E | 1.885 | 0.99 |
| 114_S | 117_K | 1.862 | 0.99 |
| 178_T | 193_V | 1.854 | 0.99 |
| 310_S | 316_E | 1.850 | 0.99 |
| 247_P | 304_L | 1.846 | 0.99 |
| 556_L | 572_G | 1.824 | 0.99 |
| 339_H | 648_Y | 1.816 | 0.99 |
| 119_E | 196_Y | 1.811 | 0.99 |
| 612_G | 626_E | 1.809 | 0.99 |
| 627_V | 639_N | 1.791 | 0.99 |
| 466_I | 482_S | 1.788 | 0.99 |
| 515_I | 637_L | 1.787 | 0.99 |
| 492_L | 508_I | 1.784 | 0.99 |
| 143_H | 156_K | 1.781 | 0.99 |
| 186_E | 603_P | 1.763 | 0.99 |
| 652_V | 658_V | 1.757 | 0.99 |
| 161_F | 180_Q | 1.735 | 0.99 |
| 25_E | 28_Q | 1.731 | 0.99 |
| 522_V | 638_L | 1.709 | 0.98 |
| 23_L | 94_A | 1.701 | 0.98 |
| 536_S | 622_H | 1.695 | 0.98 |
| 193_V | 203_C | 1.690 | 0.98 |
| 337_Y | 346_F | 1.673 | 0.98 |
| 71_V | 74_Q | 1.673 | 0.98 |
| 115_D | 143_H | 1.672 | 0.98 |
| 593_I | 646_I | 1.671 | 0.98 |
| 64_K | 106_T | 1.657 | 0.98 |
| 131_Y | 135_R | 1.657 | 0.98 |
| 174_L | 203_C | 1.653 | 0.98 |
| 263_E | 304_L | 1.648 | 0.98 |
| 575_A | 605_V | 1.646 | 0.98 |
| 272_F | 304_L | 1.635 | 0.98 |
| 133_A | 186_E | 1.630 | 0.98 |
| 175_N | 298_H | 1.620 | 0.98 |
| 204_D | 247_P | 1.619 | 0.98 |
| 66_T | 105_K | 1.614 | 0.98 |
| 413_V | 443_A | 1.611 | 0.98 |
| 272_F | 303_E | 1.606 | 0.97 |
| 558_G | 643_L | 1.606 | 0.97 |
| 527_N | 530_K | 1.606 | 0.97 |
| 385_I | 420_V | 1.594 | 0.97 |
| 306_I | 320_R | 1.591 | 0.97 |
| 66_T | 104_P | 1.590 | 0.97 |
| 120_F | 162_Y | 1.584 | 0.97 |
| 20_I | 40_I | 1.584 | 0.97 |
| 182_L | 185_L | 1.572 | 0.97 |
| 120_F | 195_S | 1.568 | 0.97 |
| 594_A | 609_I | 1.556 | 0.97 |
| 493_S | 497_D | 1.551 | 0.97 |
| 289_L | 304_L | 1.539 | 0.96 |
| 406_E | 410_R | 1.533 | 0.96 |
| 419_C | 438_C | 1.530 | 0.96 |
| 60_S | 121_I | 1.528 | 0.96 |
| 602_F | 613_D | 1.516 | 0.96 |
| 161_F | 181_V | 1.508 | 0.96 |
| 114_S | 143_H | 1.503 | 0.96 |
| 511_G | 518_Q | 1.495 | 0.96 |
| 115_D | 159_K | 1.492 | 0.96 |
| 291_L | 297_A | 1.490 | 0.96 |
| 423_S | 456_M | 1.482 | 0.95 |
| 75_K | 106_T | 1.482 | 0.95 |
| 176_E | 179_K | 1.479 | 0.95 |
| 445_T | 460_T | 1.471 | 0.95 |
| 42_V | 89_N | 1.461 | 0.95 |
| 361_D | 364_N | 1.440 | 0.94 |
| 649_W | 653_N | 1.437 | 0.94 |
| 292_E | 320_R | 1.426 | 0.94 |
| 496_N | 505_H | 1.420 | 0.94 |
| 327_M | 332_I | 1.419 | 0.94 |
| 448_I | 490_F | 1.419 | 0.94 |
| 612_G | 629_E | 1.416 | 0.94 |
| 414_F | 417_D | 1.411 | 0.94 |
| 546_L | 594_A | 1.408 | 0.93 |
| 437_Y | 440_E | 1.406 | 0.93 |
| 174_L | 195_S | 1.398 | 0.93 |
| 195_S | 198_Y | 1.395 | 0.93 |
| 287_K | 322_I | 1.393 | 0.93 |
| 181_V | 185_L | 1.385 | 0.93 |
| 298_H | 305_R | 1.385 | 0.93 |
| 91_V | 200_G | 1.380 | 0.93 |
| 162_Y | 195_S | 1.379 | 0.92 |
| 429_A | 433_L | 1.374 | 0.92 |
| 43_D | 194_K | 1.361 | 0.92 |
| 543_L | 593_I | 1.360 | 0.92 |
| 351_S | 482_S | 1.355 | 0.92 |
| 8_V | 91_V | 1.355 | 0.92 |
| 63_V | 75_K | 1.348 | 0.91 |
| 177_L | 181_V | 1.337 | 0.91 |
| 17_G | 273_F | 1.334 | 0.91 |
| 200_G | 301_D | 1.330 | 0.91 |
| 552_F | 556_L | 1.329 | 0.91 |
| 192_L | 274_L | 1.328 | 0.91 |
| 175_N | 179_K | 1.328 | 0.91 |
| 447_G | 456_M | 1.325 | 0.90 |
| 419_C | 443_A | 1.321 | 0.90 |
| 278_P | 290_F | 1.321 | 0.90 |
| 162_Y | 197_H | 1.319 | 0.90 |
| 286_K | 324_T | 1.318 | 0.90 |
| 122_V | 154_I | 1.306 | 0.90 |
| 630_T | 638_L | 1.305 | 0.89 |
| 517_E | 520_K | 1.303 | 0.89 |
| 525_L | 528_K | 1.299 | 0.89 |
| 41_A | 62_I | 1.297 | 0.89 |
| 378_T | 444_L | 1.293 | 0.89 |
| 194_K | 202_V | 1.290 | 0.89 |
| 541_K | 654_R | 1.282 | 0.88 |
| 447_G | 463_G | 1.281 | 0.88 |
| 263_E | 272_F | 1.277 | 0.88 |
| 268_M | 271_E | 1.270 | 0.88 |
| 289_L | 306_I | 1.263 | 0.87 |
| 66_T | 103_Q | 1.263 | 0.87 |
| 394_Y | 398_L | 1.260 | 0.87 |
| 334_K | 660_F | 1.246 | 0.86 |
| 449_V | 457_S | 1.244 | 0.86 |
| 137_Y | 160_H | 1.242 | 0.86 |
| 514_K | 518_Q | 1.238 | 0.86 |
| 274_L | 297_A | 1.235 | 0.86 |
| 518_Q | 638_L | 1.232 | 0.86 |
| 466_I | 483_Q | 1.231 | 0.85 |
| 534_N | 653_N | 1.229 | 0.85 |
| 7_Y | 15_S | 1.220 | 0.85 |
| 201_E | 300_Y | 1.219 | 0.85 |
| 7_Y | 19_I | 1.216 | 0.84 |
| 492_L | 495_S | 1.211 | 0.84 |
| 300_Y | 303_E | 1.210 | 0.84 |
| 136_K | 140_S | 1.209 | 0.84 |
| 586_V | 592_I | 1.204 | 0.84 |
| 405_E | 409_R | 1.200 | 0.83 |
| 49_D | 58_M | 1.198 | 0.83 |
| 70_K | 73_K | 1.196 | 0.83 |
| 15_S | 19_I | 1.195 | 0.83 |
| 307_H | 317_S | 1.187 | 0.83 |
| 531_D | 534_N | 1.184 | 0.82 |
| 262_S | 285_T | 1.182 | 0.82 |
| 359_R | 489_M | 1.180 | 0.82 |
| 176_E | 180_Q | 1.178 | 0.82 |
| 551_Q | 595_F | 1.176 | 0.82 |
| 43_D | 91_V | 1.173 | 0.81 |
| 382_C | 417_D | 1.173 | 0.81 |
| 546_L | 555_A | 1.168 | 0.81 |
| 278_P | 282_V | 1.167 | 0.81 |
| 279_A | 282_V | 1.159 | 0.80 |
| 41_A | 121_I | 1.156 | 0.80 |
| 537_L | 646_I | 1.152 | 0.80 |
| 342_Q | 346_F | 1.147 | 0.79 |
| 439_L | 461_H | 1.146 | 0.79 |
| 24_I | 76_I | 1.145 | 0.79 |
| 407_L | 633_C | 1.144 | 0.79 |
| 350_D | 520_K | 1.139 | 0.79 |
| 614_A | 617_S | 1.135 | 0.78 |
| 511_G | 631_V | 1.126 | 0.78 |
| 179_K | 307_H | 1.125 | 0.78 |
| 554_T | 640_V | 1.116 | 0.77 |
| 537_L | 622_H | 1.114 | 0.77 |
| 138_L | 145_F | 1.111 | 0.76 |
| 24_I | 73_K | 1.110 | 0.76 |
| 7_Y | 22_N | 1.107 | 0.76 |
| 457_S | 463_G | 1.107 | 0.76 |
| 175_N | 296_I | 1.106 | 0.76 |
| 182_L | 205_K | 1.101 | 0.75 |
| 578_L | 583_L | 1.087 | 0.74 |
| 103_Q | 148_E | 1.082 | 0.74 |
| 274_L | 299_I | 1.081 | 0.74 |
| 348_Q | 481_T | 1.081 | 0.74 |
| 604_K | 671_E | 1.080 | 0.73 |
| 515_I | 638_L | 1.079 | 0.73 |
| 385_I | 418_T | 1.078 | 0.73 |
| 68_K | 657_D | 1.075 | 0.73 |
| 113_K | 121_I | 1.074 | 0.73 |
| 645_L | 649_W | 1.074 | 0.73 |
| 68_K | 334_K | 1.072 | 0.73 |
| 492_L | 505_H | 1.071 | 0.73 |
| 452_V | 465_H | 1.070 | 0.72 |
| 20_I | 89_N | 1.070 | 0.72 |
| 129_T | 604_K | 1.065 | 0.72 |
| 420_V | 490_F | 1.064 | 0.72 |
| 275_S | 280_S | 1.063 | 0.72 |
| 392_T | 476_S | 1.063 | 0.72 |
| 554_T | 638_L | 1.063 | 0.72 |
| 525_L | 625_L | 1.060 | 0.71 |
| 8_V | 301_D | 1.059 | 0.71 |
| 507_E | 631_V | 1.057 | 0.71 |
| 179_K | 296_I | 1.057 | 0.71 |
| 421_F | 460_T | 1.054 | 0.71 |
| 164_L | 180_Q | 1.049 | 0.70 |
| 400_T | 403_I | 1.049 | 0.70 |
| 646_I | 650_L | 1.048 | 0.70 |
| 376_L | 380_R | 1.047 | 0.70 |
| 485_I | 512_L | 1.041 | 0.69 |
| 6_G | 274_L | 1.039 | 0.69 |
| 139_L | 148_E | 1.039 | 0.69 |
| 138_L | 157_L | 1.039 | 0.69 |
| 493_S | 496_N | 1.038 | 0.69 |
| 514_K | 517_E | 1.037 | 0.69 |
| 64_K | 113_K | 1.035 | 0.69 |
| 400_T | 487_L | 1.033 | 0.69 |
| 542_S | 590_L | 1.029 | 0.68 |
| 403_I | 488_V | 1.023 | 0.68 |
| 544_L | 590_L | 1.023 | 0.68 |
| 457_S | 465_H | 1.021 | 0.67 |
| 448_I | 466_I | 1.020 | 0.67 |
| 1_M | 4_I | 1.018 | 0.67 |
| 174_L | 193_V | 1.016 | 0.67 |
| 545_L | 562_I | 1.014 | 0.67 |
| 518_Q | 630_T | 1.013 | 0.66 |
| 66_T | 106_T | 1.009 | 0.66 |
| 387_M | 420_V | 1.009 | 0.66 |
| 448_I | 487_L | 1.005 | 0.66 |
| 136_K | 139_L | 1.004 | 0.65 |
| 511_G | 514_K | 1.004 | 0.65 |
| 41_A | 60_S | 1.004 | 0.65 |
| 353_F | 520_K | 1.003 | 0.65 |
| 518_Q | 522_V | 1.002 | 0.65 |
| 62_I | 113_K | 1.000 | 0.65 |
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 | |
| 2bplA | 3 | 0.8614 | 100 | 0.41 | Contact Map |
| 2zj3A | 1 | 0.5022 | 100 | 0.638 | Contact Map |
| 2pocA | 4 | 0.4829 | 100 | 0.64 | Contact Map |
| 3tbfA | 8 | 0.4873 | 100 | 0.642 | Contact Map |
| 1moqA | 1 | 0.5007 | 100 | 0.643 | Contact Map |
| 3fj1A | 4 | 0.4575 | 100 | 0.694 | Contact Map |
| 3knzA | 6 | 0.4396 | 100 | 0.694 | Contact Map |
| 1j5xA | 1 | 0.4441 | 100 | 0.695 | Contact Map |
| 2e5fA | 2 | 0.4441 | 100 | 0.701 | Contact Map |
| 2amlA | 2 | 0.4888 | 100 | 0.703 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)