| erra |
| ID: | 1484045552 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 423 (351) | ||
| Sequences: | 622 (336.7) | ||
| Seq/Len: | 1.772 | ||
| Nf(neff/√len): | 18.0 |
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: 1.772).
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 |
| 106_T | 136_F | 2.831 | 1.00 |
| 413_L | 416_E | 2.309 | 1.00 |
| 91_Y | 98_A | 2.198 | 0.99 |
| 97_E | 100_K | 1.969 | 0.98 |
| 136_F | 140_L | 1.898 | 0.98 |
| 134_C | 144_M | 1.895 | 0.98 |
| 89_Y | 108_Q | 1.889 | 0.98 |
| 79_C | 82_C | 1.848 | 0.97 |
| 91_Y | 100_K | 1.820 | 0.97 |
| 99_C | 102_F | 1.794 | 0.97 |
| 135_R | 144_M | 1.772 | 0.96 |
| 97_E | 132_Q | 1.757 | 0.96 |
| 119_N | 133_A | 1.732 | 0.96 |
| 236_I | 242_W | 1.727 | 0.96 |
| 236_I | 406_G | 1.684 | 0.95 |
| 139_C | 144_M | 1.655 | 0.94 |
| 104_K | 265_W | 1.647 | 0.94 |
| 86_A | 95_S | 1.636 | 0.94 |
| 133_A | 137_T | 1.615 | 0.93 |
| 96_C | 99_C | 1.611 | 0.93 |
| 138_K | 144_M | 1.546 | 0.91 |
| 98_A | 101_A | 1.525 | 0.90 |
| 90_H | 103_F | 1.524 | 0.90 |
| 108_Q | 150_R | 1.524 | 0.90 |
| 84_D | 87_S | 1.512 | 0.90 |
| 78_L | 86_A | 1.507 | 0.89 |
| 98_A | 109_G | 1.499 | 0.89 |
| 99_C | 103_F | 1.493 | 0.89 |
| 134_C | 139_C | 1.488 | 0.89 |
| 198_V | 202_L | 1.484 | 0.89 |
| 104_K | 156_G | 1.482 | 0.88 |
| 90_H | 99_C | 1.479 | 0.88 |
| 90_H | 102_F | 1.472 | 0.88 |
| 267_E | 389_R | 1.469 | 0.88 |
| 149_V | 153_R | 1.435 | 0.86 |
| 236_I | 265_W | 1.425 | 0.86 |
| 79_C | 96_C | 1.419 | 0.85 |
| 84_D | 91_Y | 1.415 | 0.85 |
| 96_C | 102_F | 1.409 | 0.85 |
| 258_M | 262_Q | 1.407 | 0.85 |
| 134_C | 138_K | 1.397 | 0.84 |
| 134_C | 143_G | 1.395 | 0.84 |
| 211_A | 214_D | 1.384 | 0.83 |
| 325_E | 377_R | 1.381 | 0.83 |
| 265_W | 334_L | 1.379 | 0.83 |
| 319_L | 330_K | 1.373 | 0.83 |
| 95_S | 124_T | 1.365 | 0.82 |
| 152_D | 156_G | 1.354 | 0.81 |
| 87_S | 97_E | 1.338 | 0.80 |
| 242_W | 265_W | 1.336 | 0.80 |
| 111_I | 132_Q | 1.328 | 0.80 |
| 271_L | 329_L | 1.328 | 0.80 |
| 83_G | 100_K | 1.324 | 0.79 |
| 135_R | 139_C | 1.323 | 0.79 |
| 81_V | 142_V | 1.309 | 0.78 |
| 135_R | 138_K | 1.300 | 0.78 |
| 108_Q | 152_D | 1.298 | 0.78 |
| 81_V | 160_K | 1.293 | 0.77 |
| 101_A | 109_G | 1.293 | 0.77 |
| 98_A | 129_K | 1.292 | 0.77 |
| 106_T | 275_Q | 1.291 | 0.77 |
| 128_R | 144_M | 1.290 | 0.77 |
| 91_Y | 101_A | 1.286 | 0.77 |
| 121_C | 134_C | 1.285 | 0.77 |
| 104_K | 262_Q | 1.284 | 0.76 |
| 249_F | 257_Q | 1.282 | 0.76 |
| 104_K | 117_A | 1.280 | 0.76 |
| 87_S | 104_K | 1.278 | 0.76 |
| 98_A | 124_T | 1.274 | 0.76 |
| 82_C | 99_C | 1.272 | 0.76 |
| 86_A | 93_V | 1.268 | 0.75 |
| 332_L | 346_E | 1.259 | 0.74 |
| 131_C | 134_C | 1.258 | 0.74 |
| 91_Y | 99_C | 1.250 | 0.74 |
| 121_C | 144_M | 1.250 | 0.74 |
| 173_P | 180_P | 1.249 | 0.74 |
| 79_C | 103_F | 1.247 | 0.73 |
| 131_C | 144_M | 1.246 | 0.73 |
| 103_F | 135_R | 1.237 | 0.73 |
| 121_C | 139_C | 1.229 | 0.72 |
| 329_L | 362_Y | 1.227 | 0.72 |
| 113_Y | 128_R | 1.224 | 0.71 |
| 132_Q | 389_R | 1.221 | 0.71 |
| 92_G | 102_F | 1.219 | 0.71 |
| 82_C | 90_H | 1.216 | 0.71 |
| 96_C | 103_F | 1.215 | 0.71 |
| 249_F | 261_L | 1.210 | 0.70 |
| 248_G | 286_F | 1.210 | 0.70 |
| 98_A | 132_Q | 1.209 | 0.70 |
| 257_Q | 260_V | 1.209 | 0.70 |
| 242_W | 277_S | 1.206 | 0.70 |
| 91_Y | 102_F | 1.205 | 0.70 |
| 92_G | 99_C | 1.201 | 0.69 |
| 238_V | 316_L | 1.200 | 0.69 |
| 322_E | 362_Y | 1.196 | 0.69 |
| 79_C | 90_H | 1.191 | 0.68 |
| 362_Y | 397_A | 1.189 | 0.68 |
| 119_N | 129_K | 1.188 | 0.68 |
| 401_G | 405_E | 1.181 | 0.68 |
| 104_K | 268_V | 1.180 | 0.67 |
| 152_D | 160_K | 1.176 | 0.67 |
| 240_I | 244_K | 1.174 | 0.67 |
| 82_C | 96_C | 1.172 | 0.67 |
| 79_C | 135_R | 1.168 | 0.66 |
| 104_K | 241_S | 1.167 | 0.66 |
| 82_C | 103_F | 1.167 | 0.66 |
| 79_C | 99_C | 1.165 | 0.66 |
| 90_H | 96_C | 1.160 | 0.66 |
| 100_K | 276_R | 1.160 | 0.66 |
| 92_G | 103_F | 1.156 | 0.65 |
| 128_R | 139_C | 1.153 | 0.65 |
| 349_E | 378_A | 1.152 | 0.65 |
| 265_W | 330_K | 1.147 | 0.64 |
| 82_C | 102_F | 1.143 | 0.64 |
| 103_F | 144_M | 1.139 | 0.63 |
| 79_C | 102_F | 1.137 | 0.63 |
| 181_L | 185_G | 1.136 | 0.63 |
| 123_I | 128_R | 1.131 | 0.63 |
| 256_D | 342_I | 1.128 | 0.62 |
| 412_K | 415_L | 1.127 | 0.62 |
| 101_A | 130_A | 1.125 | 0.62 |
| 140_L | 147_E | 1.122 | 0.62 |
| 382_L | 389_R | 1.120 | 0.62 |
| 103_F | 134_C | 1.109 | 0.60 |
| 128_R | 134_C | 1.108 | 0.60 |
| 84_D | 97_E | 1.107 | 0.60 |
| 138_K | 143_G | 1.106 | 0.60 |
| 106_T | 126_R | 1.103 | 0.60 |
| 108_Q | 129_K | 1.099 | 0.59 |
| 92_G | 96_C | 1.099 | 0.59 |
| 201_L | 205_E | 1.098 | 0.59 |
| 132_Q | 154_V | 1.096 | 0.59 |
| 325_E | 329_L | 1.094 | 0.59 |
| 101_A | 129_K | 1.085 | 0.58 |
| 135_R | 143_G | 1.083 | 0.58 |
| 244_K | 257_Q | 1.081 | 0.57 |
| 326_Y | 330_K | 1.080 | 0.57 |
| 121_C | 138_K | 1.079 | 0.57 |
| 356_H | 382_L | 1.073 | 0.57 |
| 158_R | 161_Y | 1.069 | 0.56 |
| 294_E | 331_A | 1.067 | 0.56 |
| 381_L | 400_Y | 1.066 | 0.56 |
| 342_I | 362_Y | 1.065 | 0.56 |
| 90_H | 100_K | 1.065 | 0.56 |
| 78_L | 258_M | 1.062 | 0.55 |
| 98_A | 161_Y | 1.062 | 0.55 |
| 104_K | 275_Q | 1.060 | 0.55 |
| 136_F | 157_G | 1.060 | 0.55 |
| 112_E | 133_A | 1.058 | 0.55 |
| 119_N | 123_I | 1.057 | 0.55 |
| 350_Q | 353_E | 1.054 | 0.55 |
| 86_A | 109_G | 1.050 | 0.54 |
| 343_E | 347_A | 1.049 | 0.54 |
| 112_E | 146_K | 1.049 | 0.54 |
| 113_Y | 129_K | 1.046 | 0.54 |
| 131_C | 143_G | 1.044 | 0.53 |
| 320_R | 348_V | 1.038 | 0.53 |
| 96_C | 135_R | 1.036 | 0.53 |
| 382_L | 409_P | 1.036 | 0.53 |
| 165_P | 176_F | 1.032 | 0.52 |
| 89_Y | 94_A | 1.032 | 0.52 |
| 93_V | 246_I | 1.030 | 0.52 |
| 132_Q | 146_K | 1.027 | 0.52 |
| 183_V | 186_G | 1.026 | 0.52 |
| 156_G | 161_Y | 1.024 | 0.51 |
| 131_C | 139_C | 1.019 | 0.51 |
| 313_V | 329_L | 1.019 | 0.51 |
| 180_P | 186_G | 1.016 | 0.50 |
| 377_R | 386_P | 1.015 | 0.50 |
| 97_E | 389_R | 1.014 | 0.50 |
| 179_G | 185_G | 1.014 | 0.50 |
| 319_L | 363_E | 1.014 | 0.50 |
| 85_V | 101_A | 1.012 | 0.50 |
| 194_V | 217_G | 1.012 | 0.50 |
| 328_L | 355_L | 1.012 | 0.50 |
| 104_K | 127_R | 1.011 | 0.50 |
| 106_T | 152_D | 1.010 | 0.50 |
| 254_L | 258_M | 1.008 | 0.50 |
| 150_R | 156_G | 1.006 | 0.49 |
| 121_C | 143_G | 1.005 | 0.49 |
| 89_Y | 150_R | 1.003 | 0.49 |
| 87_S | 91_Y | 1.002 | 0.49 |
| 180_P | 185_G | 1.001 | 0.49 |
| 151_L | 154_V | 1.001 | 0.49 |
| 267_E | 382_L | 1.000 | 0.49 |
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 | |
| 3dzyA | 1 | 0.7116 | 100 | 0.395 | Contact Map |
| 4nqaB | 2 | 0.8251 | 100 | 0.42 | Contact Map |
| 3dzyD | 1 | 0.7612 | 100 | 0.439 | Contact Map |
| 4iqrA | 4 | 0.7541 | 100 | 0.452 | Contact Map |
| 3vi8A | 1 | 0.5957 | 100 | 0.64 | Contact Map |
| 1lbdA | 1 | 0.5508 | 100 | 0.641 | Contact Map |
| 1z5xE | 1 | 0.539 | 100 | 0.659 | Contact Map |
| 1xdkB | 2 | 0.539 | 100 | 0.669 | Contact Map |
| 3k6pA | 1 | 0.5343 | 100 | 0.671 | Contact Map |
| 1ovlA | 6 | 0.5626 | 100 | 0.672 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)