| SMOX |
| ID: | 1484911324 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 555 (493) | ||
| Sequences: | 908 (597) | ||
| Seq/Len: | 1.842 | ||
| Nf(neff/√len): | 26.9 |
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: 1.842).
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 |
| 39_A | 329_I | 3.095 | 1.00 |
| 539_E | 542_R | 3.066 | 1.00 |
| 260_P | 477_Y | 2.956 | 1.00 |
| 29_V | 53_V | 2.681 | 1.00 |
| 34_L | 529_T | 2.590 | 1.00 |
| 441_D | 471_A | 2.575 | 1.00 |
| 440_D | 443_A | 2.530 | 1.00 |
| 329_I | 543_L | 2.516 | 1.00 |
| 331_T | 517_S | 2.503 | 1.00 |
| 26_R | 50_D | 2.496 | 1.00 |
| 57_S | 478_F | 2.371 | 1.00 |
| 57_S | 475_N | 2.354 | 1.00 |
| 26_R | 326_D | 2.348 | 1.00 |
| 56_A | 477_Y | 2.346 | 1.00 |
| 517_S | 539_E | 2.218 | 1.00 |
| 28_V | 54_L | 2.186 | 0.99 |
| 60_I | 257_L | 2.183 | 0.99 |
| 31_G | 36_G | 2.136 | 0.99 |
| 57_S | 65_Q | 2.125 | 0.99 |
| 536_G | 540_A | 2.093 | 0.99 |
| 239_F | 529_T | 2.071 | 0.99 |
| 89_I | 533_L | 2.012 | 0.99 |
| 330_V | 514_V | 2.006 | 0.99 |
| 251_P | 256_Q | 1.934 | 0.98 |
| 33_G | 36_G | 1.908 | 0.98 |
| 28_V | 325_A | 1.807 | 0.97 |
| 353_K | 516_F | 1.804 | 0.97 |
| 444_V | 469_R | 1.789 | 0.97 |
| 41_R | 45_E | 1.776 | 0.97 |
| 339_R | 479_R | 1.767 | 0.97 |
| 167_S | 487_V | 1.758 | 0.96 |
| 359_R | 493_D | 1.727 | 0.96 |
| 27_V | 33_G | 1.721 | 0.96 |
| 521_T | 538_R | 1.698 | 0.95 |
| 30_I | 33_G | 1.677 | 0.95 |
| 431_E | 434_L | 1.670 | 0.95 |
| 83_G | 87_N | 1.655 | 0.95 |
| 337_L | 357_I | 1.635 | 0.94 |
| 57_S | 333_S | 1.632 | 0.94 |
| 30_I | 330_V | 1.626 | 0.94 |
| 35_A | 440_D | 1.625 | 0.94 |
| 89_I | 242_V | 1.585 | 0.93 |
| 28_V | 323_I | 1.573 | 0.92 |
| 32_A | 60_I | 1.565 | 0.92 |
| 347_P | 350_P | 1.555 | 0.92 |
| 34_L | 64_V | 1.555 | 0.92 |
| 334_L | 357_I | 1.538 | 0.91 |
| 263_C | 346_R | 1.538 | 0.91 |
| 28_V | 315_V | 1.530 | 0.91 |
| 29_V | 33_G | 1.525 | 0.91 |
| 372_F | 449_T | 1.523 | 0.91 |
| 263_C | 316_E | 1.503 | 0.90 |
| 197_M | 201_Y | 1.493 | 0.90 |
| 58_S | 257_L | 1.487 | 0.89 |
| 29_V | 250_I | 1.439 | 0.87 |
| 259_K | 319_D | 1.439 | 0.87 |
| 31_G | 40_A | 1.436 | 0.87 |
| 334_L | 337_L | 1.436 | 0.87 |
| 66_S | 76_L | 1.426 | 0.86 |
| 314_V | 324_P | 1.426 | 0.86 |
| 235_I | 242_V | 1.425 | 0.86 |
| 345_F | 516_F | 1.420 | 0.86 |
| 347_P | 536_G | 1.419 | 0.86 |
| 55_E | 59_H | 1.418 | 0.86 |
| 370_L | 441_D | 1.401 | 0.85 |
| 338_K | 357_I | 1.391 | 0.85 |
| 25_P | 52_T | 1.386 | 0.84 |
| 334_L | 360_L | 1.383 | 0.84 |
| 138_E | 442_E | 1.383 | 0.84 |
| 26_R | 52_T | 1.376 | 0.84 |
| 54_L | 325_A | 1.372 | 0.83 |
| 33_G | 37_L | 1.371 | 0.83 |
| 33_G | 40_A | 1.371 | 0.83 |
| 350_P | 501_L | 1.350 | 0.82 |
| 78_A | 529_T | 1.349 | 0.82 |
| 32_A | 331_T | 1.336 | 0.81 |
| 500_P | 542_R | 1.336 | 0.81 |
| 532_A | 536_G | 1.327 | 0.81 |
| 327_H | 513_Q | 1.321 | 0.80 |
| 133_K | 137_E | 1.321 | 0.80 |
| 424_L | 430_G | 1.321 | 0.80 |
| 66_S | 73_T | 1.314 | 0.80 |
| 360_L | 497_L | 1.313 | 0.80 |
| 437_E | 530_H | 1.301 | 0.79 |
| 28_V | 540_A | 1.296 | 0.78 |
| 525_Y | 530_H | 1.289 | 0.78 |
| 87_N | 530_H | 1.287 | 0.78 |
| 93_A | 242_V | 1.281 | 0.77 |
| 244_E | 264_I | 1.279 | 0.77 |
| 173_R | 191_K | 1.276 | 0.77 |
| 316_E | 322_V | 1.264 | 0.76 |
| 30_I | 487_V | 1.261 | 0.76 |
| 345_F | 353_K | 1.251 | 0.75 |
| 366_D | 530_H | 1.249 | 0.75 |
| 27_V | 31_G | 1.242 | 0.74 |
| 331_T | 337_L | 1.237 | 0.74 |
| 371_E | 466_R | 1.236 | 0.74 |
| 318_E | 476_P | 1.234 | 0.73 |
| 475_N | 478_F | 1.226 | 0.73 |
| 237_S | 241_R | 1.223 | 0.72 |
| 52_T | 326_D | 1.214 | 0.72 |
| 66_S | 75_E | 1.212 | 0.72 |
| 32_A | 37_L | 1.211 | 0.71 |
| 30_I | 332_V | 1.210 | 0.71 |
| 366_D | 437_E | 1.204 | 0.71 |
| 453_R | 462_P | 1.200 | 0.70 |
| 259_K | 317_C | 1.199 | 0.70 |
| 356_A | 519_E | 1.198 | 0.70 |
| 64_V | 243_V | 1.194 | 0.70 |
| 347_P | 353_K | 1.192 | 0.70 |
| 75_E | 470_S | 1.190 | 0.70 |
| 528_T | 535_S | 1.188 | 0.69 |
| 533_L | 537_Q | 1.185 | 0.69 |
| 75_E | 480_G | 1.185 | 0.69 |
| 30_I | 261_V | 1.183 | 0.69 |
| 34_L | 246_L | 1.183 | 0.69 |
| 238_G | 261_V | 1.180 | 0.69 |
| 30_I | 264_I | 1.178 | 0.68 |
| 36_G | 40_A | 1.178 | 0.68 |
| 334_L | 363_G | 1.175 | 0.68 |
| 63_R | 334_L | 1.174 | 0.68 |
| 453_R | 463_K | 1.173 | 0.68 |
| 134_D | 545_E | 1.172 | 0.68 |
| 264_I | 267_D | 1.171 | 0.68 |
| 258_G | 379_P | 1.169 | 0.68 |
| 197_M | 200_Q | 1.168 | 0.67 |
| 68_R | 240_M | 1.166 | 0.67 |
| 471_A | 474_S | 1.166 | 0.67 |
| 63_R | 519_E | 1.165 | 0.67 |
| 329_I | 461_I | 1.163 | 0.67 |
| 27_V | 40_A | 1.163 | 0.67 |
| 265_H | 346_R | 1.161 | 0.67 |
| 333_S | 478_F | 1.161 | 0.67 |
| 239_F | 482_Y | 1.157 | 0.66 |
| 256_Q | 264_I | 1.149 | 0.66 |
| 54_L | 323_I | 1.147 | 0.65 |
| 522_H | 527_S | 1.147 | 0.65 |
| 331_T | 476_P | 1.143 | 0.65 |
| 218_S | 222_F | 1.139 | 0.65 |
| 449_T | 461_I | 1.138 | 0.65 |
| 259_K | 323_I | 1.138 | 0.65 |
| 445_A | 467_I | 1.138 | 0.65 |
| 29_V | 316_E | 1.137 | 0.64 |
| 51_V | 333_S | 1.133 | 0.64 |
| 261_V | 264_I | 1.133 | 0.64 |
| 335_G | 338_K | 1.132 | 0.64 |
| 30_I | 355_A | 1.119 | 0.63 |
| 495_E | 523_R | 1.118 | 0.62 |
| 162_A | 258_G | 1.118 | 0.62 |
| 63_R | 480_G | 1.118 | 0.62 |
| 478_F | 517_S | 1.116 | 0.62 |
| 426_G | 530_H | 1.116 | 0.62 |
| 334_L | 338_K | 1.115 | 0.62 |
| 335_G | 519_E | 1.114 | 0.62 |
| 28_V | 39_A | 1.111 | 0.62 |
| 238_G | 246_L | 1.111 | 0.62 |
| 63_R | 377_W | 1.111 | 0.62 |
| 28_V | 52_T | 1.111 | 0.62 |
| 313_V | 328_V | 1.108 | 0.61 |
| 332_V | 343_S | 1.107 | 0.61 |
| 218_S | 363_G | 1.105 | 0.61 |
| 42_A | 537_Q | 1.104 | 0.61 |
| 329_I | 368_I | 1.102 | 0.61 |
| 446_E | 450_E | 1.099 | 0.61 |
| 79_T | 365_T | 1.099 | 0.61 |
| 482_Y | 519_E | 1.094 | 0.60 |
| 325_A | 345_F | 1.093 | 0.60 |
| 55_E | 61_G | 1.092 | 0.60 |
| 316_E | 450_E | 1.092 | 0.60 |
| 34_L | 243_V | 1.091 | 0.60 |
| 51_V | 325_A | 1.090 | 0.60 |
| 333_S | 475_N | 1.090 | 0.60 |
| 518_G | 521_T | 1.083 | 0.59 |
| 32_A | 36_G | 1.081 | 0.59 |
| 59_H | 65_Q | 1.081 | 0.59 |
| 483_S | 516_F | 1.078 | 0.58 |
| 437_E | 483_S | 1.077 | 0.58 |
| 42_A | 46_Q | 1.077 | 0.58 |
| 364_T | 433_A | 1.076 | 0.58 |
| 263_C | 514_V | 1.071 | 0.58 |
| 517_S | 540_A | 1.069 | 0.57 |
| 43_L | 55_E | 1.067 | 0.57 |
| 63_R | 367_K | 1.067 | 0.57 |
| 368_I | 426_G | 1.067 | 0.57 |
| 80_W | 526_Y | 1.065 | 0.57 |
| 89_I | 537_Q | 1.065 | 0.57 |
| 41_R | 249_G | 1.065 | 0.57 |
| 57_S | 470_S | 1.065 | 0.57 |
| 88_P | 376_F | 1.064 | 0.57 |
| 363_G | 531_G | 1.064 | 0.57 |
| 367_K | 519_E | 1.064 | 0.57 |
| 315_V | 355_A | 1.062 | 0.57 |
| 265_H | 316_E | 1.062 | 0.57 |
| 355_A | 359_R | 1.062 | 0.57 |
| 87_N | 334_L | 1.058 | 0.56 |
| 95_A | 368_I | 1.057 | 0.56 |
| 53_V | 255_I | 1.056 | 0.56 |
| 52_T | 256_Q | 1.056 | 0.56 |
| 37_L | 53_V | 1.052 | 0.56 |
| 345_F | 521_T | 1.048 | 0.55 |
| 217_V | 223_G | 1.046 | 0.55 |
| 325_A | 530_H | 1.045 | 0.55 |
| 30_I | 255_I | 1.045 | 0.55 |
| 81_I | 89_I | 1.045 | 0.55 |
| 35_A | 517_S | 1.043 | 0.55 |
| 140_S | 148_N | 1.043 | 0.55 |
| 518_G | 535_S | 1.042 | 0.54 |
| 39_A | 47_G | 1.042 | 0.54 |
| 88_P | 537_Q | 1.041 | 0.54 |
| 37_L | 60_I | 1.039 | 0.54 |
| 256_Q | 323_I | 1.038 | 0.54 |
| 531_G | 536_G | 1.036 | 0.54 |
| 334_L | 361_G | 1.033 | 0.53 |
| 81_I | 94_E | 1.032 | 0.53 |
| 525_Y | 528_T | 1.031 | 0.53 |
| 86_G | 530_H | 1.031 | 0.53 |
| 316_E | 545_E | 1.030 | 0.53 |
| 75_E | 79_T | 1.028 | 0.53 |
| 147_Y | 153_F | 1.025 | 0.53 |
| 24_Q | 324_P | 1.025 | 0.53 |
| 32_A | 47_G | 1.025 | 0.53 |
| 388_W | 455_F | 1.025 | 0.53 |
| 29_V | 40_A | 1.021 | 0.52 |
| 92_L | 132_P | 1.021 | 0.52 |
| 245_L | 248_E | 1.021 | 0.52 |
| 367_K | 377_W | 1.019 | 0.52 |
| 539_E | 543_L | 1.017 | 0.52 |
| 516_F | 521_T | 1.016 | 0.52 |
| 139_F | 257_L | 1.010 | 0.51 |
| 472_W | 519_E | 1.010 | 0.51 |
| 363_G | 480_G | 1.010 | 0.51 |
| 471_A | 483_S | 1.008 | 0.51 |
| 63_R | 331_T | 1.006 | 0.51 |
| 494_V | 526_Y | 1.004 | 0.50 |
| 360_L | 423_V | 1.002 | 0.50 |
| 425_S | 433_A | 1.000 | 0.50 |
| 409_C | 414_L | 1.000 | 0.50 |
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 | |
| 2z3yA | 1 | 0.8378 | 100 | 0.483 | Contact Map |
| 3zn0A | 1 | 0.8559 | 100 | 0.485 | Contact Map |
| 1rsgA | 2 | 0.8072 | 100 | 0.507 | Contact Map |
| 1b37A | 3 | 0.791 | 100 | 0.524 | Contact Map |
| 1s3eA | 2 | 0.7766 | 100 | 0.531 | Contact Map |
| 4hsuA | 1 | 0.8216 | 100 | 0.533 | Contact Map |
| 4i59A | 4 | 0.7568 | 100 | 0.538 | Contact Map |
| 2yg5A | 1 | 0.7622 | 100 | 0.542 | Contact Map |
| 3x0vA | 2 | 0.8216 | 100 | 0.565 | Contact Map |
| 3ayjA | 2 | 0.8865 | 100 | 0.57 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)