| 4n56 |
| ID: | 1471567671 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 522 (418) | ||
| Sequences: | 3225 (1841.2) | ||
| Seq/Len: | 7.715 | ||
| Nf(neff/√len): | 90.1 |
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: 7.715).
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 |
| 402_E | 406_R | 4.760 | 1.00 |
| 364_R | 368_E | 4.079 | 1.00 |
| 177_H | 458_F | 4.051 | 1.00 |
| 207_E | 265_K | 3.891 | 1.00 |
| 276_K | 281_D | 3.269 | 1.00 |
| 162_W | 166_E | 3.149 | 1.00 |
| 412_L | 445_T | 3.135 | 1.00 |
| 187_V | 287_I | 3.005 | 1.00 |
| 196_E | 327_R | 2.969 | 1.00 |
| 339_L | 514_E | 2.900 | 1.00 |
| 394_A | 398_K | 2.803 | 1.00 |
| 164_Y | 169_R | 2.764 | 1.00 |
| 493_K | 497_E | 2.754 | 1.00 |
| 226_R | 230_D | 2.709 | 1.00 |
| 200_E | 268_Q | 2.648 | 1.00 |
| 200_E | 203_R | 2.618 | 1.00 |
| 460_R | 495_V | 2.535 | 1.00 |
| 111_A | 121_P | 2.531 | 1.00 |
| 339_L | 482_K | 2.470 | 1.00 |
| 393_R | 397_E | 2.407 | 1.00 |
| 468_M | 478_L | 2.406 | 1.00 |
| 369_G | 507_E | 2.393 | 1.00 |
| 155_E | 161_L | 2.353 | 1.00 |
| 212_A | 262_I | 2.352 | 1.00 |
| 338_W | 481_P | 2.307 | 1.00 |
| 105_D | 110_L | 2.290 | 1.00 |
| 167_V | 413_F | 2.243 | 1.00 |
| 227_V | 231_E | 2.232 | 1.00 |
| 208_V | 218_L | 2.230 | 1.00 |
| 337_G | 482_K | 2.220 | 1.00 |
| 201_I | 273_T | 2.174 | 1.00 |
| 105_D | 164_Y | 2.171 | 1.00 |
| 202_A | 205_E | 2.165 | 1.00 |
| 184_R | 335_E | 2.164 | 1.00 |
| 214_H | 231_E | 2.114 | 1.00 |
| 478_L | 492_A | 2.084 | 1.00 |
| 341_V | 480_A | 2.065 | 1.00 |
| 358_G | 363_I | 2.055 | 1.00 |
| 161_L | 165_R | 2.028 | 1.00 |
| 193_L | 197_V | 1.976 | 1.00 |
| 494_E | 498_G | 1.929 | 1.00 |
| 189_Y | 330_R | 1.924 | 1.00 |
| 481_P | 484_R | 1.923 | 1.00 |
| 398_K | 402_E | 1.915 | 1.00 |
| 109_L | 301_T | 1.912 | 1.00 |
| 466_A | 484_R | 1.904 | 1.00 |
| 485_A | 512_I | 1.897 | 1.00 |
| 183_V | 469_L | 1.881 | 1.00 |
| 177_H | 462_E | 1.879 | 1.00 |
| 257_R | 264_E | 1.876 | 1.00 |
| 401_E | 405_R | 1.873 | 1.00 |
| 135_E | 139_R | 1.872 | 1.00 |
| 485_A | 489_A | 1.866 | 1.00 |
| 458_F | 462_E | 1.864 | 1.00 |
| 194_S | 281_D | 1.860 | 1.00 |
| 149_N | 153_R | 1.854 | 1.00 |
| 391_K | 394_A | 1.854 | 1.00 |
| 456_K | 459_P | 1.845 | 1.00 |
| 478_L | 488_V | 1.816 | 1.00 |
| 460_R | 494_E | 1.816 | 1.00 |
| 139_R | 143_S | 1.814 | 1.00 |
| 299_N | 311_S | 1.810 | 1.00 |
| 376_T | 382_N | 1.780 | 1.00 |
| 264_E | 268_Q | 1.778 | 1.00 |
| 490_R | 494_E | 1.771 | 1.00 |
| 408_Y | 416_R | 1.767 | 1.00 |
| 460_R | 463_E | 1.765 | 1.00 |
| 153_R | 156_G | 1.764 | 1.00 |
| 452_L | 456_K | 1.739 | 1.00 |
| 181_T | 467_R | 1.711 | 1.00 |
| 198_A | 276_K | 1.692 | 1.00 |
| 466_A | 488_V | 1.654 | 1.00 |
| 353_L | 386_L | 1.651 | 1.00 |
| 226_R | 231_E | 1.647 | 1.00 |
| 219_N | 269_Y | 1.646 | 1.00 |
| 190_L | 331_A | 1.643 | 1.00 |
| 206_A | 210_R | 1.629 | 1.00 |
| 107_P | 139_R | 1.625 | 1.00 |
| 410_E | 416_R | 1.622 | 1.00 |
| 360_E | 391_K | 1.622 | 1.00 |
| 352_V | 442_V | 1.607 | 1.00 |
| 358_G | 503_A | 1.599 | 1.00 |
| 125_A | 142_L | 1.595 | 1.00 |
| 456_K | 495_V | 1.593 | 1.00 |
| 209_F | 218_L | 1.591 | 1.00 |
| 189_Y | 192_A | 1.586 | 1.00 |
| 370_R | 375_E | 1.582 | 1.00 |
| 486_E | 489_A | 1.570 | 1.00 |
| 147_F | 151_W | 1.563 | 1.00 |
| 107_P | 143_S | 1.559 | 1.00 |
| 397_E | 400_L | 1.555 | 1.00 |
| 488_V | 492_A | 1.548 | 1.00 |
| 461_L | 488_V | 1.544 | 1.00 |
| 330_R | 517_L | 1.538 | 1.00 |
| 514_E | 518_S | 1.537 | 1.00 |
| 360_E | 364_R | 1.529 | 1.00 |
| 363_I | 367_Q | 1.524 | 1.00 |
| 422_L | 433_A | 1.517 | 1.00 |
| 167_V | 452_L | 1.511 | 1.00 |
| 174_V | 455_V | 1.505 | 0.99 |
| 184_R | 333_I | 1.502 | 0.99 |
| 427_K | 430_R | 1.501 | 0.99 |
| 459_P | 463_E | 1.498 | 0.99 |
| 460_R | 491_L | 1.494 | 0.99 |
| 186_D | 333_I | 1.492 | 0.99 |
| 491_L | 495_V | 1.491 | 0.99 |
| 489_A | 493_K | 1.489 | 0.99 |
| 480_A | 488_V | 1.476 | 0.99 |
| 497_E | 507_E | 1.472 | 0.99 |
| 141_A | 145_R | 1.464 | 0.99 |
| 404_R | 434_E | 1.446 | 0.99 |
| 207_E | 210_R | 1.433 | 0.99 |
| 257_R | 263_V | 1.431 | 0.99 |
| 465_G | 484_R | 1.428 | 0.99 |
| 200_E | 324_L | 1.425 | 0.99 |
| 198_A | 202_A | 1.424 | 0.99 |
| 232_L | 260_H | 1.404 | 0.99 |
| 482_K | 514_E | 1.398 | 0.99 |
| 457_L | 495_V | 1.389 | 0.99 |
| 419_V | 433_A | 1.387 | 0.99 |
| 298_F | 470_L | 1.381 | 0.99 |
| 335_E | 338_W | 1.373 | 0.99 |
| 203_R | 207_E | 1.369 | 0.99 |
| 432_A | 436_M | 1.363 | 0.99 |
| 413_F | 500_Y | 1.362 | 0.99 |
| 355_H | 502_L | 1.353 | 0.99 |
| 343_L | 510_V | 1.335 | 0.98 |
| 152_G | 156_G | 1.322 | 0.98 |
| 204_L | 265_K | 1.313 | 0.98 |
| 189_Y | 331_A | 1.313 | 0.98 |
| 404_R | 430_R | 1.300 | 0.98 |
| 112_Y | 302_A | 1.296 | 0.98 |
| 457_L | 478_L | 1.293 | 0.98 |
| 188_A | 192_A | 1.284 | 0.98 |
| 187_V | 191_R | 1.284 | 0.98 |
| 489_A | 512_I | 1.282 | 0.98 |
| 427_K | 431_E | 1.282 | 0.98 |
| 110_L | 164_Y | 1.279 | 0.98 |
| 486_E | 490_R | 1.269 | 0.98 |
| 338_W | 479_E | 1.264 | 0.98 |
| 174_V | 458_F | 1.262 | 0.98 |
| 465_G | 483_E | 1.260 | 0.98 |
| 401_E | 404_R | 1.257 | 0.98 |
| 296_T | 310_S | 1.255 | 0.98 |
| 343_L | 508_V | 1.255 | 0.98 |
| 293_R | 335_E | 1.255 | 0.98 |
| 151_W | 155_E | 1.255 | 0.98 |
| 466_A | 481_P | 1.254 | 0.97 |
| 493_K | 510_V | 1.254 | 0.97 |
| 109_L | 172_S | 1.250 | 0.97 |
| 184_R | 334_A | 1.248 | 0.97 |
| 465_G | 481_P | 1.246 | 0.97 |
| 339_L | 512_I | 1.238 | 0.97 |
| 334_A | 340_L | 1.238 | 0.97 |
| 185_L | 287_I | 1.232 | 0.97 |
| 191_R | 284_P | 1.217 | 0.97 |
| 209_F | 215_P | 1.217 | 0.97 |
| 341_V | 492_A | 1.203 | 0.97 |
| 511_G | 520_K | 1.199 | 0.96 |
| 169_R | 172_S | 1.198 | 0.96 |
| 410_E | 414_G | 1.196 | 0.96 |
| 258_E | 264_E | 1.195 | 0.96 |
| 191_R | 195_L | 1.183 | 0.96 |
| 194_S | 280_I | 1.179 | 0.96 |
| 222_D | 226_R | 1.177 | 0.96 |
| 396_L | 438_F | 1.173 | 0.96 |
| 341_V | 485_A | 1.171 | 0.96 |
| 183_V | 340_L | 1.165 | 0.96 |
| 136_A | 140_A | 1.162 | 0.96 |
| 327_R | 330_R | 1.159 | 0.95 |
| 261_P | 264_E | 1.149 | 0.95 |
| 183_V | 470_L | 1.144 | 0.95 |
| 411_T | 444_G | 1.143 | 0.95 |
| 449_L | 506_L | 1.131 | 0.95 |
| 208_V | 265_K | 1.127 | 0.95 |
| 340_L | 477_V | 1.126 | 0.94 |
| 197_V | 280_I | 1.121 | 0.94 |
| 198_A | 281_D | 1.118 | 0.94 |
| 338_W | 467_R | 1.116 | 0.94 |
| 249_S | 252_V | 1.111 | 0.94 |
| 135_E | 143_S | 1.109 | 0.94 |
| 219_N | 273_T | 1.101 | 0.94 |
| 122_E | 139_R | 1.086 | 0.93 |
| 353_L | 392_V | 1.085 | 0.93 |
| 201_I | 272_L | 1.083 | 0.93 |
| 163_L | 167_V | 1.080 | 0.93 |
| 250_A | 254_E | 1.074 | 0.92 |
| 216_F | 227_V | 1.070 | 0.92 |
| 188_A | 191_R | 1.068 | 0.92 |
| 124_V | 146_L | 1.067 | 0.92 |
| 413_F | 452_L | 1.063 | 0.92 |
| 515_D | 518_S | 1.059 | 0.92 |
| 195_L | 199_E | 1.056 | 0.92 |
| 498_G | 501_P | 1.051 | 0.91 |
| 399_T | 402_E | 1.050 | 0.91 |
| 511_G | 519_A | 1.047 | 0.91 |
| 430_R | 434_E | 1.046 | 0.91 |
| 364_R | 367_Q | 1.042 | 0.91 |
| 196_E | 200_E | 1.040 | 0.91 |
| 151_W | 165_R | 1.036 | 0.91 |
| 208_V | 262_I | 1.035 | 0.91 |
| 480_A | 485_A | 1.034 | 0.90 |
| 159_R | 410_E | 1.032 | 0.90 |
| 421_D | 433_A | 1.026 | 0.90 |
| 194_S | 276_K | 1.024 | 0.90 |
| 330_R | 518_S | 1.023 | 0.90 |
| 209_F | 214_H | 1.013 | 0.89 |
| 406_R | 410_E | 1.004 | 0.89 |
| 136_A | 139_R | 1.000 | 0.88 |
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 | 0.9349 | 100 | 0.307 | Contact Map |
| 1bgxT | 1 | 0.9789 | 100 | 0.307 | Contact Map |
| 4bwjA | 1 | 0.9004 | 100 | 0.317 | Contact Map |
| 4x0qA | 2 | 0.9042 | 100 | 0.321 | Contact Map |
| 4yfuA | 2 | 0 | 100 | 0.321 | Contact Map |
| 4xvkA | 1 | 0.8985 | 100 | 0.323 | Contact Map |
| 1x9mA | 1 | 0.908 | 100 | 0.366 | Contact Map |
| 3ikmA | 2 | 0.8908 | 100 | 0.663 | Contact Map |
| 1yt3A | 1 | 0.592 | 99.9 | 0.857 | Contact Map |
| 2e6mA | 1 | 0.251 | 98.7 | 0.933 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)