| 500 |
| ID: | 1393511077 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 324 (324) | ||
| Sequences: | 410 (305.5) | ||
| Seq/Len: | 1.265 | ||
| Nf(neff/√len): | 17.0 |
HHblits Results: (2013_03)
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: 1.265).
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 |
| 309_P | 312_P | 3.788 | 1.00 |
| 308_D | 311_R | 3.020 | 1.00 |
| 308_D | 312_P | 2.829 | 1.00 |
| 65_R | 127_D | 2.354 | 0.99 |
| 217_I | 227_V | 2.344 | 0.99 |
| 306_E | 312_P | 2.190 | 0.99 |
| 71_L | 197_V | 2.131 | 0.98 |
| 150_I | 164_I | 2.078 | 0.98 |
| 16_F | 183_F | 2.072 | 0.98 |
| 35_V | 56_I | 1.948 | 0.97 |
| 34_Y | 55_V | 1.942 | 0.96 |
| 172_P | 186_V | 1.939 | 0.96 |
| 132_V | 207_M | 1.923 | 0.96 |
| 144_S | 167_E | 1.898 | 0.96 |
| 34_Y | 300_R | 1.864 | 0.95 |
| 265_F | 279_L | 1.840 | 0.95 |
| 136_I | 229_I | 1.791 | 0.94 |
| 303_E | 323_L | 1.760 | 0.93 |
| 70_L | 290_D | 1.754 | 0.93 |
| 122_I | 231_L | 1.746 | 0.93 |
| 307_T | 311_R | 1.730 | 0.92 |
| 239_I | 267_A | 1.727 | 0.92 |
| 90_L | 160_L | 1.724 | 0.92 |
| 112_V | 152_V | 1.707 | 0.91 |
| 31_M | 56_I | 1.669 | 0.90 |
| 220_D | 223_E | 1.652 | 0.90 |
| 165_E | 226_A | 1.612 | 0.88 |
| 306_E | 309_P | 1.584 | 0.87 |
| 258_R | 297_T | 1.577 | 0.87 |
| 76_L | 206_E | 1.568 | 0.86 |
| 17_V | 182_R | 1.567 | 0.86 |
| 246_V | 253_L | 1.533 | 0.84 |
| 144_S | 148_G | 1.527 | 0.84 |
| 208_I | 229_I | 1.526 | 0.84 |
| 133_L | 164_I | 1.502 | 0.83 |
| 171_I | 179_I | 1.497 | 0.82 |
| 180_F | 215_I | 1.472 | 0.81 |
| 70_L | 211_H | 1.463 | 0.80 |
| 143_Y | 185_R | 1.437 | 0.79 |
| 277_E | 281_E | 1.436 | 0.79 |
| 62_R | 191_S | 1.433 | 0.78 |
| 269_N | 272_H | 1.386 | 0.75 |
| 97_T | 176_L | 1.377 | 0.74 |
| 33_S | 55_V | 1.375 | 0.74 |
| 33_S | 63_M | 1.373 | 0.74 |
| 236_E | 249_G | 1.368 | 0.74 |
| 298_V | 305_V | 1.338 | 0.71 |
| 290_D | 300_R | 1.324 | 0.70 |
| 303_E | 317_R | 1.321 | 0.70 |
| 97_T | 137_L | 1.321 | 0.70 |
| 18_A | 146_A | 1.313 | 0.69 |
| 162_L | 229_I | 1.309 | 0.69 |
| 239_I | 246_V | 1.306 | 0.69 |
| 273_V | 300_R | 1.298 | 0.68 |
| 245_S | 252_L | 1.297 | 0.68 |
| 70_L | 202_S | 1.293 | 0.68 |
| 41_G | 49_A | 1.289 | 0.67 |
| 19_N | 29_T | 1.283 | 0.67 |
| 307_T | 312_P | 1.281 | 0.67 |
| 39_I | 324_L | 1.278 | 0.66 |
| 208_I | 237_L | 1.277 | 0.66 |
| 306_E | 310_S | 1.263 | 0.65 |
| 30_T | 67_V | 1.260 | 0.65 |
| 213_G | 231_L | 1.248 | 0.64 |
| 255_L | 301_L | 1.246 | 0.63 |
| 292_R | 295_D | 1.243 | 0.63 |
| 317_R | 323_L | 1.239 | 0.63 |
| 276_R | 295_D | 1.231 | 0.62 |
| 283_V | 303_E | 1.226 | 0.62 |
| 172_P | 188_K | 1.213 | 0.60 |
| 205_R | 209_L | 1.213 | 0.60 |
| 270_K | 274_L | 1.207 | 0.60 |
| 3_V | 7_E | 1.201 | 0.59 |
| 257_N | 261_E | 1.199 | 0.59 |
| 276_R | 292_R | 1.197 | 0.59 |
| 257_N | 300_R | 1.187 | 0.58 |
| 59_E | 73_L | 1.183 | 0.57 |
| 67_V | 227_V | 1.183 | 0.57 |
| 63_M | 206_E | 1.181 | 0.57 |
| 176_L | 217_I | 1.181 | 0.57 |
| 18_A | 181_K | 1.169 | 0.56 |
| 55_V | 318_R | 1.164 | 0.56 |
| 258_R | 283_V | 1.158 | 0.55 |
| 236_E | 313_Y | 1.154 | 0.55 |
| 163_V | 226_A | 1.141 | 0.53 |
| 258_R | 284_W | 1.140 | 0.53 |
| 30_T | 227_V | 1.138 | 0.53 |
| 34_Y | 318_R | 1.137 | 0.53 |
| 136_I | 164_I | 1.137 | 0.53 |
| 177_K | 191_S | 1.135 | 0.53 |
| 204_T | 215_I | 1.130 | 0.52 |
| 160_L | 233_L | 1.130 | 0.52 |
| 235_G | 298_V | 1.123 | 0.52 |
| 59_E | 185_R | 1.116 | 0.51 |
| 124_A | 129_L | 1.105 | 0.50 |
| 284_W | 288_Y | 1.102 | 0.50 |
| 283_V | 300_R | 1.100 | 0.49 |
| 173_K | 219_S | 1.100 | 0.49 |
| 188_K | 192_R | 1.100 | 0.49 |
| 133_L | 137_L | 1.100 | 0.49 |
| 17_V | 73_L | 1.099 | 0.49 |
| 219_S | 223_E | 1.098 | 0.49 |
| 63_M | 297_T | 1.097 | 0.49 |
| 12_D | 37_T | 1.093 | 0.49 |
| 178_H | 181_K | 1.077 | 0.47 |
| 237_L | 267_A | 1.076 | 0.47 |
| 192_R | 195_G | 1.075 | 0.47 |
| 24_L | 318_R | 1.074 | 0.47 |
| 34_Y | 37_T | 1.071 | 0.46 |
| 60_T | 124_A | 1.069 | 0.46 |
| 63_M | 77_D | 1.068 | 0.46 |
| 24_L | 59_E | 1.064 | 0.46 |
| 185_R | 190_R | 1.061 | 0.45 |
| 258_R | 300_R | 1.057 | 0.45 |
| 288_Y | 300_R | 1.055 | 0.45 |
| 274_L | 324_L | 1.053 | 0.45 |
| 133_L | 154_A | 1.051 | 0.45 |
| 13_R | 182_R | 1.050 | 0.44 |
| 77_D | 303_E | 1.049 | 0.44 |
| 97_T | 130_T | 1.048 | 0.44 |
| 297_T | 300_R | 1.045 | 0.44 |
| 125_D | 128_M | 1.043 | 0.44 |
| 171_I | 225_T | 1.040 | 0.43 |
| 261_E | 300_R | 1.033 | 0.43 |
| 37_T | 55_V | 1.032 | 0.43 |
| 38_L | 170_G | 1.032 | 0.43 |
| 127_D | 183_F | 1.029 | 0.42 |
| 297_T | 317_R | 1.029 | 0.42 |
| 151_K | 165_E | 1.029 | 0.42 |
| 16_F | 171_I | 1.027 | 0.42 |
| 238_R | 247_Y | 1.026 | 0.42 |
| 277_E | 316_T | 1.025 | 0.42 |
| 33_S | 303_E | 1.020 | 0.42 |
| 104_Q | 142_K | 1.019 | 0.41 |
| 258_R | 290_D | 1.018 | 0.41 |
| 34_Y | 315_L | 1.017 | 0.41 |
| 18_A | 131_Q | 1.016 | 0.41 |
| 37_T | 318_R | 1.015 | 0.41 |
| 315_L | 323_L | 1.015 | 0.41 |
| 129_L | 202_S | 1.013 | 0.41 |
| 184_Y | 190_R | 1.010 | 0.41 |
| 98_I | 162_L | 1.008 | 0.40 |
| 94_I | 98_I | 1.007 | 0.40 |
| 172_P | 175_E | 1.007 | 0.40 |
| 280_L | 285_G | 1.007 | 0.40 |
| 219_S | 222_G | 1.005 | 0.40 |
| 53_L | 294_V | 1.004 | 0.40 |
| 77_D | 206_E | 1.003 | 0.40 |
| 16_F | 296_V | 1.003 | 0.40 |
| 290_D | 303_E | 1.000 | 0.40 |
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 | |
| 4i5sA | 2 | 0.6883 | 100 | 0.591 | Contact Map |
| 2c2aA | 1 | 0.6975 | 100 | 0.604 | Contact Map |
| 2e0aA | 2 | 0.7623 | 100 | 0.619 | Contact Map |
| 1y8oA | 1 | 0.8117 | 100 | 0.629 | Contact Map |
| 4mpcA | 1 | 0.7531 | 100 | 0.63 | Contact Map |
| 4e01A | 1 | 0.7006 | 100 | 0.643 | Contact Map |
| 2q8gA | 1 | 0.7747 | 100 | 0.644 | Contact Map |
| 4ew8A | 2 | 0.7037 | 100 | 0.644 | Contact Map |
| 3jz3A | 2 | 0.4969 | 100 | 0.646 | Contact Map |
| 3a0rA | 1 | 0.679 | 100 | 0.647 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)