| yidc |
| ID: | 1446043651 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 548 (545) | ||
| Sequences: | 1550 (1076.3) | ||
| Seq/Len: | 2.844 | ||
| Nf(neff/√len): | 46.1 |
HHblits Results: (2015_06)
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: 2.844).
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 |
| 407_E | 410_A | 5.578 | 1.00 |
| 410_A | 414_A | 4.158 | 1.00 |
| 351_V | 360_I | 4.154 | 1.00 |
| 391_Q | 394_R | 3.781 | 1.00 |
| 64_K | 85_P | 3.755 | 1.00 |
| 389_K | 392_A | 3.708 | 1.00 |
| 356_F | 451_F | 3.693 | 1.00 |
| 342_K | 346_W | 3.373 | 1.00 |
| 386_L | 417_V | 3.285 | 1.00 |
| 343_L | 364_I | 3.262 | 1.00 |
| 394_R | 398_G | 3.198 | 1.00 |
| 393_M | 404_I | 2.957 | 1.00 |
| 472_G | 503_T | 2.933 | 1.00 |
| 391_Q | 395_E | 2.815 | 1.00 |
| 82_A | 309_V | 2.759 | 1.00 |
| 64_K | 69_D | 2.654 | 1.00 |
| 65_T | 167_L | 2.646 | 1.00 |
| 347_I | 360_I | 2.554 | 1.00 |
| 70_L | 82_A | 2.536 | 1.00 |
| 347_I | 364_I | 2.531 | 1.00 |
| 162_T | 179_N | 2.509 | 1.00 |
| 369_M | 432_I | 2.368 | 1.00 |
| 356_F | 452_A | 2.297 | 1.00 |
| 470_L | 518_I | 2.295 | 1.00 |
| 70_L | 167_L | 2.267 | 1.00 |
| 403_R | 407_E | 2.248 | 1.00 |
| 347_I | 351_V | 2.239 | 1.00 |
| 394_R | 404_I | 2.219 | 1.00 |
| 69_D | 83_L | 2.190 | 1.00 |
| 166_V | 177_N | 2.168 | 1.00 |
| 387_Q | 391_Q | 2.163 | 1.00 |
| 261_A | 327_T | 2.149 | 1.00 |
| 467_L | 515_L | 2.135 | 1.00 |
| 403_R | 406_Q | 2.116 | 1.00 |
| 150_P | 164_T | 2.104 | 1.00 |
| 356_F | 360_I | 2.069 | 1.00 |
| 179_N | 302_A | 2.067 | 1.00 |
| 72_I | 151_M | 2.065 | 1.00 |
| 7_L | 11_A | 2.064 | 1.00 |
| 402_Q | 406_Q | 2.047 | 1.00 |
| 392_A | 396_R | 2.044 | 1.00 |
| 346_W | 350_F | 2.015 | 1.00 |
| 66_D | 170_G | 2.006 | 1.00 |
| 70_L | 79_V | 1.902 | 0.99 |
| 152_T | 162_T | 1.893 | 0.99 |
| 474_T | 521_N | 1.892 | 0.99 |
| 381_A | 384_R | 1.889 | 0.99 |
| 526_I | 530_L | 1.883 | 0.99 |
| 369_M | 428_I | 1.875 | 0.99 |
| 356_F | 359_I | 1.817 | 0.99 |
| 173_A | 320_V | 1.779 | 0.99 |
| 62_S | 69_D | 1.768 | 0.99 |
| 404_I | 408_M | 1.766 | 0.99 |
| 360_I | 363_F | 1.764 | 0.99 |
| 177_N | 304_N | 1.752 | 0.99 |
| 397_L | 403_R | 1.749 | 0.99 |
| 71_T | 81_Q | 1.744 | 0.98 |
| 364_I | 368_I | 1.723 | 0.98 |
| 469_I | 473_V | 1.709 | 0.98 |
| 360_I | 364_I | 1.686 | 0.98 |
| 470_L | 474_T | 1.674 | 0.98 |
| 448_Q | 460_A | 1.673 | 0.98 |
| 160_T | 181_Q | 1.665 | 0.98 |
| 60_L | 71_T | 1.659 | 0.98 |
| 340_L | 365_V | 1.634 | 0.97 |
| 9_V | 13_L | 1.628 | 0.97 |
| 62_S | 71_T | 1.619 | 0.97 |
| 344_L | 357_S | 1.609 | 0.97 |
| 60_L | 80_E | 1.608 | 0.97 |
| 497_F | 501_I | 1.599 | 0.97 |
| 390_I | 393_M | 1.597 | 0.97 |
| 68_L | 82_A | 1.591 | 0.97 |
| 134_E | 152_T | 1.581 | 0.97 |
| 371_P | 375_A | 1.572 | 0.97 |
| 181_Q | 300_T | 1.571 | 0.97 |
| 83_L | 98_Q | 1.557 | 0.96 |
| 398_G | 404_I | 1.546 | 0.96 |
| 61_I | 74_T | 1.544 | 0.96 |
| 177_N | 302_A | 1.534 | 0.96 |
| 480_K | 496_T | 1.532 | 0.96 |
| 63_V | 167_L | 1.531 | 0.96 |
| 168_K | 175_N | 1.518 | 0.96 |
| 69_D | 85_P | 1.511 | 0.95 |
| 473_V | 477_F | 1.507 | 0.95 |
| 77_G | 151_M | 1.501 | 0.95 |
| 67_V | 86_A | 1.495 | 0.95 |
| 398_G | 401_K | 1.495 | 0.95 |
| 366_R | 369_M | 1.495 | 0.95 |
| 308_W | 316_K | 1.493 | 0.95 |
| 63_V | 72_I | 1.489 | 0.95 |
| 340_L | 361_I | 1.484 | 0.95 |
| 393_M | 398_G | 1.478 | 0.95 |
| 81_Q | 98_Q | 1.475 | 0.95 |
| 7_L | 14_F | 1.473 | 0.95 |
| 254_A | 327_T | 1.473 | 0.95 |
| 296_Q | 299_Q | 1.468 | 0.94 |
| 434_L | 438_Y | 1.467 | 0.94 |
| 359_I | 515_L | 1.462 | 0.94 |
| 455_I | 467_L | 1.455 | 0.94 |
| 72_I | 149_V | 1.454 | 0.94 |
| 9_V | 12_L | 1.453 | 0.94 |
| 359_I | 519_V | 1.440 | 0.94 |
| 530_L | 534_G | 1.425 | 0.93 |
| 187_P | 297_P | 1.422 | 0.93 |
| 363_F | 523_V | 1.421 | 0.93 |
| 401_K | 405_S | 1.412 | 0.93 |
| 474_T | 525_I | 1.408 | 0.93 |
| 497_F | 500_V | 1.387 | 0.92 |
| 365_V | 428_I | 1.386 | 0.92 |
| 17_F | 21_Q | 1.382 | 0.92 |
| 393_M | 408_M | 1.370 | 0.91 |
| 189_E | 294_L | 1.366 | 0.91 |
| 221_A | 238_I | 1.363 | 0.91 |
| 392_A | 401_K | 1.357 | 0.91 |
| 162_T | 181_Q | 1.356 | 0.91 |
| 164_T | 179_N | 1.353 | 0.91 |
| 90_E | 94_T | 1.350 | 0.90 |
| 372_L | 510_P | 1.345 | 0.90 |
| 175_N | 304_N | 1.342 | 0.90 |
| 389_K | 415_E | 1.337 | 0.90 |
| 382_K | 385_M | 1.335 | 0.90 |
| 471_M | 478_I | 1.329 | 0.90 |
| 61_I | 133_V | 1.326 | 0.89 |
| 330_Y | 341_F | 1.323 | 0.89 |
| 68_L | 167_L | 1.316 | 0.89 |
| 500_V | 503_T | 1.314 | 0.89 |
| 315_D | 345_K | 1.310 | 0.89 |
| 438_Y | 442_G | 1.307 | 0.88 |
| 81_Q | 101_E | 1.291 | 0.88 |
| 346_W | 349_S | 1.286 | 0.87 |
| 469_I | 500_V | 1.285 | 0.87 |
| 173_A | 306_T | 1.284 | 0.87 |
| 336_I | 340_L | 1.267 | 0.86 |
| 148_Q | 164_T | 1.267 | 0.86 |
| 58_G | 73_N | 1.265 | 0.86 |
| 275_Y | 287_G | 1.263 | 0.86 |
| 196_L | 307_L | 1.261 | 0.86 |
| 410_A | 413_K | 1.261 | 0.86 |
| 471_M | 503_T | 1.260 | 0.86 |
| 20_W | 24_E | 1.254 | 0.86 |
| 7_L | 435_A | 1.240 | 0.85 |
| 148_Q | 166_V | 1.233 | 0.84 |
| 72_I | 165_F | 1.232 | 0.84 |
| 313_I | 316_K | 1.232 | 0.84 |
| 250_G | 269_D | 1.230 | 0.84 |
| 400_D | 403_R | 1.229 | 0.84 |
| 164_T | 177_N | 1.228 | 0.84 |
| 509_F | 517_Y | 1.224 | 0.84 |
| 101_E | 106_F | 1.217 | 0.83 |
| 426_L | 430_M | 1.209 | 0.83 |
| 478_I | 520_S | 1.209 | 0.83 |
| 351_V | 357_S | 1.208 | 0.83 |
| 406_Q | 410_A | 1.206 | 0.82 |
| 515_L | 519_V | 1.204 | 0.82 |
| 375_A | 378_T | 1.202 | 0.82 |
| 133_V | 152_T | 1.202 | 0.82 |
| 141_A | 146_E | 1.201 | 0.82 |
| 86_A | 172_Y | 1.195 | 0.82 |
| 522_L | 526_I | 1.193 | 0.81 |
| 430_M | 433_F | 1.193 | 0.81 |
| 87_Y | 444_V | 1.191 | 0.81 |
| 488_D | 491_Q | 1.188 | 0.81 |
| 32_Q | 35_Q | 1.188 | 0.81 |
| 340_L | 428_I | 1.185 | 0.81 |
| 260_F | 311_P | 1.182 | 0.81 |
| 133_V | 138_Y | 1.181 | 0.81 |
| 110_A | 307_L | 1.179 | 0.80 |
| 67_V | 171_D | 1.178 | 0.80 |
| 408_M | 412_Y | 1.171 | 0.80 |
| 460_A | 511_S | 1.168 | 0.80 |
| 351_V | 356_F | 1.163 | 0.79 |
| 163_K | 178_Y | 1.160 | 0.79 |
| 11_A | 15_V | 1.156 | 0.79 |
| 30_Q | 33_A | 1.155 | 0.78 |
| 393_M | 397_L | 1.153 | 0.78 |
| 56_G | 130_L | 1.150 | 0.78 |
| 540_L | 543_R | 1.141 | 0.77 |
| 343_L | 368_I | 1.139 | 0.77 |
| 503_T | 507_L | 1.139 | 0.77 |
| 134_E | 162_T | 1.135 | 0.77 |
| 463_P | 468_P | 1.134 | 0.77 |
| 12_L | 16_S | 1.134 | 0.77 |
| 160_T | 183_A | 1.128 | 0.76 |
| 376_Q | 532_Y | 1.122 | 0.76 |
| 316_K | 319_A | 1.122 | 0.76 |
| 175_N | 306_T | 1.118 | 0.75 |
| 365_V | 436_L | 1.118 | 0.75 |
| 150_P | 162_T | 1.115 | 0.75 |
| 73_N | 80_E | 1.114 | 0.75 |
| 478_I | 525_I | 1.111 | 0.75 |
| 490_M | 493_K | 1.110 | 0.75 |
| 501_I | 505_F | 1.108 | 0.74 |
| 111_Q | 195_Q | 1.106 | 0.74 |
| 472_G | 475_M | 1.106 | 0.74 |
| 345_K | 349_S | 1.106 | 0.74 |
| 67_V | 172_Y | 1.105 | 0.74 |
| 407_E | 414_A | 1.099 | 0.73 |
| 490_M | 494_I | 1.099 | 0.73 |
| 254_A | 511_S | 1.098 | 0.73 |
| 145_N | 169_R | 1.098 | 0.73 |
| 275_Y | 289_K | 1.094 | 0.73 |
| 393_M | 411_L | 1.087 | 0.72 |
| 373_T | 376_Q | 1.086 | 0.72 |
| 196_L | 262_T | 1.085 | 0.72 |
| 24_E | 27_K | 1.085 | 0.72 |
| 19_I | 23_W | 1.085 | 0.72 |
| 100_L | 262_T | 1.080 | 0.72 |
| 174_V | 390_I | 1.080 | 0.72 |
| 493_K | 496_T | 1.077 | 0.71 |
| 432_I | 523_V | 1.075 | 0.71 |
| 148_Q | 177_N | 1.074 | 0.71 |
| 19_I | 22_A | 1.071 | 0.71 |
| 65_T | 68_L | 1.070 | 0.71 |
| 32_Q | 170_G | 1.069 | 0.71 |
| 359_I | 452_A | 1.065 | 0.70 |
| 417_V | 479_Q | 1.065 | 0.70 |
| 348_H | 352_G | 1.064 | 0.70 |
| 312_E | 517_Y | 1.062 | 0.70 |
| 536_E | 539_G | 1.061 | 0.70 |
| 259_Y | 459_S | 1.059 | 0.69 |
| 166_V | 175_N | 1.056 | 0.69 |
| 89_K | 95_Q | 1.050 | 0.69 |
| 340_L | 368_I | 1.050 | 0.69 |
| 318_A | 325_D | 1.041 | 0.68 |
| 370_Y | 482_S | 1.029 | 0.66 |
| 165_F | 176_V | 1.025 | 0.66 |
| 376_Q | 520_S | 1.020 | 0.65 |
| 529_Q | 533_R | 1.020 | 0.65 |
| 6_N | 13_L | 1.019 | 0.65 |
| 386_L | 398_G | 1.015 | 0.65 |
| 461_Q | 464_Y | 1.015 | 0.65 |
| 376_Q | 380_M | 1.014 | 0.65 |
| 495_M | 506_F | 1.009 | 0.64 |
| 479_Q | 498_M | 1.007 | 0.64 |
| 113_G | 193_F | 1.005 | 0.64 |
| 461_Q | 507_L | 1.002 | 0.63 |
| 58_G | 74_T | 1.002 | 0.63 |
| 146_E | 168_K | 1.001 | 0.63 |
| 34_Q | 40_T | 1.000 | 0.63 |
| 79_V | 432_I | 1.000 | 0.63 |
| 7_L | 10_I | 1.000 | 0.63 |
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 | |
| 3wvfA | 2 | 0.8212 | 100 | 0.229 | Contact Map |
| 3wo6A | 1 | 0.3668 | 100 | 0.619 | Contact Map |
| 3blcA | 2 | 0.5055 | 100 | 0.69 | Contact Map |
| 3bs6A | 2 | 0.4745 | 100 | 0.752 | Contact Map |
| 3q1nA | 1 | 0.4708 | 6.3 | 0.986 | Contact Map |
| 2jucA | 1 | 0.0949 | 5 | 0.986 | Contact Map |
| 2ymyA | 2 | 0.0602 | 4.9 | 0.987 | Contact Map |
| 2mc7A | 1 | 0.042 | 3.7 | 0.987 | Contact Map |
| 1pi7A | 1 | 0.0347 | 3.5 | 0.987 | Contact Map |
| 1j8bA | 1 | 0.0876 | 3.5 | 0.987 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)