| A84 |
| ID: | 1485228627 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 485 (445) | ||
| Sequences: | 530 (443.7) | ||
| Seq/Len: | 1.191 | ||
| Nf(neff/√len): | 21.0 |
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: 1.191).
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 |
| 274_Y | 299_Y | 3.495 | 1.00 |
| 228_Q | 252_R | 3.485 | 1.00 |
| 193_E | 228_Q | 3.438 | 1.00 |
| 394_I | 436_S | 3.041 | 1.00 |
| 248_D | 270_R | 2.809 | 1.00 |
| 227_I | 251_V | 2.677 | 1.00 |
| 252_R | 274_Y | 2.616 | 1.00 |
| 460_D | 465_E | 2.609 | 1.00 |
| 49_A | 55_I | 2.572 | 1.00 |
| 45_A | 49_A | 2.493 | 1.00 |
| 195_N | 230_N | 2.453 | 0.99 |
| 229_Y | 253_Y | 2.385 | 0.99 |
| 153_Y | 189_Y | 2.376 | 0.99 |
| 438_D | 465_E | 2.327 | 0.99 |
| 155_Q | 193_E | 2.318 | 0.99 |
| 81_T | 107_G | 2.300 | 0.99 |
| 244_I | 251_V | 2.249 | 0.99 |
| 278_F | 303_M | 2.245 | 0.99 |
| 126_L | 129_N | 2.223 | 0.99 |
| 125_R | 157_D | 2.200 | 0.98 |
| 109_G | 132_R | 2.148 | 0.98 |
| 430_L | 436_S | 2.111 | 0.98 |
| 102_Y | 123_H | 2.088 | 0.98 |
| 289_I | 303_M | 2.062 | 0.97 |
| 370_L | 436_S | 2.019 | 0.97 |
| 270_R | 295_D | 1.939 | 0.96 |
| 370_L | 394_I | 1.926 | 0.96 |
| 256_F | 278_F | 1.926 | 0.96 |
| 460_D | 466_F | 1.916 | 0.96 |
| 104_V | 125_R | 1.834 | 0.94 |
| 438_D | 460_D | 1.783 | 0.93 |
| 57_V | 62_Y | 1.762 | 0.92 |
| 80_I | 103_I | 1.761 | 0.92 |
| 56_I | 81_T | 1.752 | 0.92 |
| 191_V | 226_T | 1.746 | 0.92 |
| 437_I | 460_D | 1.738 | 0.92 |
| 341_N | 368_N | 1.738 | 0.92 |
| 300_N | 456_R | 1.728 | 0.91 |
| 123_H | 153_Y | 1.723 | 0.91 |
| 315_I | 344_I | 1.715 | 0.91 |
| 54_T | 79_T | 1.674 | 0.89 |
| 129_N | 159_N | 1.663 | 0.89 |
| 125_R | 158_H | 1.659 | 0.89 |
| 295_D | 336_R | 1.651 | 0.89 |
| 59_D | 82_A | 1.643 | 0.88 |
| 392_G | 461_V | 1.602 | 0.86 |
| 46_V | 49_A | 1.577 | 0.85 |
| 59_D | 84_N | 1.554 | 0.84 |
| 450_D | 462_G | 1.543 | 0.84 |
| 300_N | 303_M | 1.540 | 0.83 |
| 258_S | 281_E | 1.537 | 0.83 |
| 34_I | 49_A | 1.534 | 0.83 |
| 73_T | 77_P | 1.528 | 0.83 |
| 437_I | 465_E | 1.523 | 0.82 |
| 429_R | 452_D | 1.512 | 0.82 |
| 67_I | 103_I | 1.499 | 0.81 |
| 125_R | 155_Q | 1.494 | 0.81 |
| 197_F | 232_F | 1.483 | 0.80 |
| 109_G | 130_H | 1.476 | 0.80 |
| 226_T | 252_R | 1.475 | 0.80 |
| 222_S | 270_R | 1.472 | 0.79 |
| 71_I | 101_E | 1.470 | 0.79 |
| 235_C | 259_C | 1.470 | 0.79 |
| 251_V | 263_V | 1.447 | 0.78 |
| 437_I | 466_F | 1.426 | 0.76 |
| 219_S | 328_L | 1.423 | 0.76 |
| 107_G | 128_N | 1.416 | 0.76 |
| 106_K | 127_T | 1.414 | 0.75 |
| 256_F | 263_V | 1.410 | 0.75 |
| 49_A | 103_I | 1.405 | 0.75 |
| 255_T | 279_F | 1.402 | 0.75 |
| 95_L | 105_F | 1.402 | 0.75 |
| 303_M | 344_I | 1.396 | 0.74 |
| 57_V | 108_F | 1.391 | 0.74 |
| 303_M | 306_L | 1.385 | 0.73 |
| 343_T | 463_A | 1.378 | 0.73 |
| 250_I | 272_E | 1.372 | 0.72 |
| 163_E | 199_N | 1.369 | 0.72 |
| 92_E | 112_T | 1.355 | 0.71 |
| 371_I | 395_V | 1.352 | 0.71 |
| 45_A | 55_I | 1.352 | 0.71 |
| 50_V | 53_D | 1.351 | 0.71 |
| 252_R | 275_G | 1.346 | 0.70 |
| 234_E | 258_S | 1.345 | 0.70 |
| 230_N | 254_N | 1.340 | 0.70 |
| 232_F | 256_F | 1.336 | 0.69 |
| 313_A | 316_I | 1.331 | 0.69 |
| 81_T | 106_K | 1.317 | 0.68 |
| 161_F | 197_F | 1.313 | 0.68 |
| 452_D | 464_D | 1.297 | 0.66 |
| 160_I | 198_Y | 1.282 | 0.65 |
| 291_V | 298_I | 1.275 | 0.64 |
| 253_Y | 275_G | 1.271 | 0.64 |
| 67_I | 80_I | 1.271 | 0.64 |
| 100_C | 103_I | 1.253 | 0.62 |
| 127_T | 157_D | 1.251 | 0.62 |
| 42_L | 57_V | 1.244 | 0.61 |
| 79_T | 104_V | 1.242 | 0.61 |
| 34_I | 45_A | 1.233 | 0.60 |
| 213_V | 227_I | 1.231 | 0.60 |
| 156_I | 159_N | 1.221 | 0.59 |
| 95_L | 110_I | 1.220 | 0.59 |
| 156_I | 171_I | 1.217 | 0.59 |
| 42_L | 46_V | 1.216 | 0.59 |
| 79_T | 93_G | 1.214 | 0.59 |
| 351_I | 371_I | 1.214 | 0.59 |
| 254_N | 276_N | 1.206 | 0.58 |
| 277_F | 305_G | 1.205 | 0.58 |
| 196_Y | 233_E | 1.205 | 0.58 |
| 194_Y | 229_Y | 1.204 | 0.58 |
| 301_N | 343_T | 1.204 | 0.58 |
| 255_T | 277_F | 1.203 | 0.58 |
| 56_I | 83_E | 1.201 | 0.57 |
| 155_Q | 194_Y | 1.201 | 0.57 |
| 51_P | 72_G | 1.199 | 0.57 |
| 158_H | 193_E | 1.197 | 0.57 |
| 396_S | 420_L | 1.196 | 0.57 |
| 344_I | 347_C | 1.194 | 0.57 |
| 275_G | 300_N | 1.194 | 0.57 |
| 43_E | 47_N | 1.188 | 0.56 |
| 227_I | 379_I | 1.186 | 0.56 |
| 343_T | 370_L | 1.184 | 0.56 |
| 338_E | 365_I | 1.182 | 0.56 |
| 58_A | 83_E | 1.178 | 0.55 |
| 105_F | 124_I | 1.178 | 0.55 |
| 159_N | 195_N | 1.173 | 0.55 |
| 305_G | 346_N | 1.171 | 0.54 |
| 155_Q | 158_H | 1.168 | 0.54 |
| 74_E | 432_Q | 1.168 | 0.54 |
| 119_E | 226_T | 1.168 | 0.54 |
| 67_I | 100_C | 1.167 | 0.54 |
| 155_Q | 191_V | 1.167 | 0.54 |
| 100_C | 407_I | 1.159 | 0.53 |
| 105_F | 163_E | 1.159 | 0.53 |
| 54_T | 81_T | 1.151 | 0.53 |
| 280_G | 305_G | 1.151 | 0.53 |
| 344_I | 371_I | 1.149 | 0.52 |
| 158_H | 194_Y | 1.149 | 0.52 |
| 209_E | 287_G | 1.141 | 0.52 |
| 32_N | 35_Y | 1.141 | 0.52 |
| 90_F | 104_V | 1.140 | 0.51 |
| 222_S | 248_D | 1.138 | 0.51 |
| 439_S | 461_V | 1.136 | 0.51 |
| 288_G | 301_N | 1.134 | 0.51 |
| 97_F | 124_I | 1.129 | 0.50 |
| 456_R | 465_E | 1.129 | 0.50 |
| 200_I | 210_A | 1.128 | 0.50 |
| 55_I | 421_E | 1.124 | 0.50 |
| 432_Q | 439_S | 1.121 | 0.50 |
| 300_N | 341_N | 1.117 | 0.49 |
| 84_N | 88_A | 1.113 | 0.49 |
| 156_I | 161_F | 1.111 | 0.49 |
| 72_G | 102_Y | 1.092 | 0.47 |
| 45_A | 57_V | 1.091 | 0.47 |
| 104_V | 344_I | 1.086 | 0.46 |
| 66_K | 339_V | 1.085 | 0.46 |
| 55_I | 58_A | 1.083 | 0.46 |
| 151_S | 240_E | 1.081 | 0.46 |
| 368_N | 440_S | 1.078 | 0.45 |
| 421_E | 433_D | 1.076 | 0.45 |
| 191_V | 228_Q | 1.068 | 0.44 |
| 110_I | 131_I | 1.067 | 0.44 |
| 34_I | 55_I | 1.067 | 0.44 |
| 153_Y | 325_S | 1.066 | 0.44 |
| 46_V | 300_N | 1.065 | 0.44 |
| 53_D | 78_I | 1.064 | 0.44 |
| 157_D | 193_E | 1.063 | 0.44 |
| 63_E | 93_G | 1.061 | 0.44 |
| 224_Y | 248_D | 1.060 | 0.44 |
| 97_F | 100_C | 1.059 | 0.44 |
| 197_F | 256_F | 1.057 | 0.43 |
| 197_F | 243_S | 1.056 | 0.43 |
| 272_E | 297_K | 1.053 | 0.43 |
| 104_V | 123_H | 1.047 | 0.42 |
| 231_L | 257_R | 1.042 | 0.42 |
| 90_F | 234_E | 1.042 | 0.42 |
| 59_D | 83_E | 1.035 | 0.41 |
| 107_G | 196_Y | 1.034 | 0.41 |
| 97_F | 376_N | 1.034 | 0.41 |
| 91_D | 111_Y | 1.034 | 0.41 |
| 248_D | 368_N | 1.034 | 0.41 |
| 299_Y | 340_V | 1.033 | 0.41 |
| 198_Y | 233_E | 1.030 | 0.41 |
| 453_G | 463_A | 1.028 | 0.41 |
| 323_D | 326_G | 1.028 | 0.41 |
| 101_E | 122_N | 1.028 | 0.41 |
| 44_D | 79_T | 1.026 | 0.40 |
| 265_L | 273_V | 1.020 | 0.40 |
| 300_N | 306_L | 1.019 | 0.40 |
| 278_F | 281_E | 1.017 | 0.40 |
| 240_E | 261_G | 1.016 | 0.40 |
| 75_D | 410_D | 1.016 | 0.40 |
| 117_K | 156_I | 1.016 | 0.40 |
| 301_N | 369_N | 1.015 | 0.39 |
| 368_N | 392_G | 1.014 | 0.39 |
| 140_S | 226_T | 1.013 | 0.39 |
| 202_P | 205_D | 1.013 | 0.39 |
| 230_N | 276_N | 1.011 | 0.39 |
| 272_E | 299_Y | 1.010 | 0.39 |
| 199_N | 234_E | 1.009 | 0.39 |
| 276_N | 301_N | 1.009 | 0.39 |
| 450_D | 453_G | 1.008 | 0.39 |
| 72_G | 77_P | 1.007 | 0.39 |
| 192_I | 227_I | 1.005 | 0.39 |
| 194_Y | 228_Q | 1.004 | 0.38 |
| 153_Y | 224_Y | 1.003 | 0.38 |
| 69_N | 100_C | 1.000 | 0.38 |
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 | |
| 1dbgA | 1 | 0.8392 | 100 | 0.569 | Contact Map |
| 1ru4A | 1 | 0.7361 | 100 | 0.64 | Contact Map |
| 3vsvA | 4 | 0.8454 | 100 | 0.693 | Contact Map |
| 2inuA | 3 | 0.6577 | 99.9 | 0.792 | Contact Map |
| 4nk6A | 1 | 0.6825 | 99.8 | 0.803 | Contact Map |
| 2pygA | 2 | 0.6804 | 99.8 | 0.804 | Contact Map |
| 1czfA | 2 | 0.6 | 99.4 | 0.859 | Contact Map |
| 3zscA | 1 | 0.6041 | 99.4 | 0.862 | Contact Map |
| 4mr0A | 2 | 0.734 | 99.3 | 0.868 | Contact Map |
| 2uvfA | 2 | 0.7052 | 99.3 | 0.868 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)