| cdhit |
| ID: | 1393552071 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 324 (324) | ||
| Sequences: | 405 (305.3) | ||
| Seq/Len: | 1.250 | ||
| 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: 1.250).
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 | 3.789 | 1.00 |
| 308_T | 311_R | 3.009 | 1.00 |
| 308_T | 312_P | 2.834 | 1.00 |
| 64_R | 126_D | 2.367 | 0.99 |
| 217_A | 227_F | 2.331 | 0.99 |
| 306_E | 312_P | 2.161 | 0.98 |
| 70_L | 197_T | 2.141 | 0.98 |
| 149_V | 164_I | 2.109 | 0.98 |
| 16_F | 183_F | 2.069 | 0.98 |
| 172_P | 186_V | 1.959 | 0.97 |
| 35_L | 55_S | 1.953 | 0.97 |
| 34_Y | 54_V | 1.950 | 0.96 |
| 131_V | 207_I | 1.926 | 0.96 |
| 143_S | 167_Q | 1.895 | 0.96 |
| 34_Y | 300_R | 1.865 | 0.95 |
| 265_H | 279_L | 1.829 | 0.94 |
| 135_I | 229_I | 1.805 | 0.94 |
| 303_E | 323_Y | 1.762 | 0.93 |
| 69_L | 290_D | 1.756 | 0.93 |
| 239_I | 267_A | 1.732 | 0.92 |
| 307_D | 311_R | 1.731 | 0.92 |
| 89_F | 160_L | 1.722 | 0.92 |
| 121_I | 231_L | 1.717 | 0.92 |
| 111_I | 151_V | 1.689 | 0.91 |
| 220_E | 223_E | 1.666 | 0.90 |
| 31_V | 55_S | 1.644 | 0.89 |
| 165_S | 226_T | 1.615 | 0.88 |
| 258_R | 297_T | 1.582 | 0.87 |
| 17_V | 182_R | 1.569 | 0.86 |
| 306_E | 309_P | 1.564 | 0.86 |
| 75_I | 206_E | 1.561 | 0.86 |
| 246_A | 253_V | 1.540 | 0.84 |
| 208_V | 229_I | 1.535 | 0.84 |
| 143_S | 147_G | 1.530 | 0.84 |
| 132_I | 164_I | 1.509 | 0.83 |
| 180_F | 215_I | 1.475 | 0.81 |
| 69_L | 211_H | 1.462 | 0.80 |
| 171_I | 179_I | 1.446 | 0.79 |
| 142_Y | 185_R | 1.433 | 0.78 |
| 61_R | 191_S | 1.427 | 0.78 |
| 277_E | 281_E | 1.425 | 0.78 |
| 269_H | 272_Q | 1.391 | 0.75 |
| 96_I | 176_L | 1.391 | 0.75 |
| 236_D | 249_R | 1.384 | 0.75 |
| 33_S | 54_V | 1.378 | 0.74 |
| 33_S | 62_M | 1.370 | 0.74 |
| 290_D | 300_R | 1.324 | 0.70 |
| 303_E | 317_R | 1.323 | 0.70 |
| 18_S | 145_D | 1.314 | 0.69 |
| 96_I | 136_L | 1.311 | 0.69 |
| 298_V | 305_I | 1.310 | 0.69 |
| 239_I | 246_A | 1.306 | 0.68 |
| 69_L | 202_A | 1.301 | 0.68 |
| 273_V | 300_R | 1.293 | 0.67 |
| 41_G | 48_A | 1.290 | 0.67 |
| 162_L | 229_I | 1.288 | 0.67 |
| 245_V | 252_E | 1.285 | 0.67 |
| 19_N | 29_T | 1.282 | 0.66 |
| 307_D | 312_P | 1.280 | 0.66 |
| 39_D | 324_M | 1.279 | 0.66 |
| 208_V | 237_L | 1.274 | 0.66 |
| 30_S | 66_I | 1.263 | 0.65 |
| 306_E | 310_S | 1.252 | 0.64 |
| 213_G | 231_L | 1.249 | 0.63 |
| 255_L | 301_L | 1.240 | 0.62 |
| 317_R | 323_Y | 1.235 | 0.62 |
| 292_R | 295_D | 1.227 | 0.61 |
| 205_K | 209_K | 1.226 | 0.61 |
| 276_R | 295_D | 1.222 | 0.61 |
| 283_V | 303_E | 1.222 | 0.61 |
| 176_L | 217_A | 1.216 | 0.60 |
| 172_P | 188_K | 1.212 | 0.60 |
| 270_T | 274_M | 1.208 | 0.59 |
| 3_A | 7_E | 1.208 | 0.59 |
| 66_I | 227_F | 1.205 | 0.59 |
| 257_H | 261_E | 1.198 | 0.59 |
| 276_R | 292_R | 1.190 | 0.58 |
| 257_H | 300_R | 1.186 | 0.57 |
| 58_E | 72_L | 1.184 | 0.57 |
| 62_M | 206_E | 1.183 | 0.57 |
| 54_V | 318_R | 1.171 | 0.56 |
| 18_S | 181_D | 1.166 | 0.55 |
| 236_D | 313_Y | 1.157 | 0.55 |
| 258_R | 283_V | 1.151 | 0.54 |
| 177_P | 191_S | 1.144 | 0.53 |
| 163_S | 226_T | 1.144 | 0.53 |
| 34_Y | 318_R | 1.143 | 0.53 |
| 258_R | 284_W | 1.142 | 0.53 |
| 30_S | 227_F | 1.137 | 0.53 |
| 204_A | 215_I | 1.124 | 0.51 |
| 160_L | 233_Y | 1.123 | 0.51 |
| 135_I | 164_I | 1.123 | 0.51 |
| 188_K | 192_R | 1.119 | 0.51 |
| 58_E | 185_R | 1.115 | 0.50 |
| 284_W | 288_Y | 1.112 | 0.50 |
| 123_I | 128_M | 1.103 | 0.49 |
| 219_S | 223_E | 1.099 | 0.49 |
| 235_G | 298_V | 1.099 | 0.49 |
| 283_V | 300_R | 1.096 | 0.49 |
| 62_M | 297_T | 1.096 | 0.49 |
| 17_V | 72_L | 1.092 | 0.48 |
| 132_I | 136_L | 1.091 | 0.48 |
| 237_L | 267_A | 1.090 | 0.48 |
| 12_E | 37_A | 1.090 | 0.48 |
| 173_K | 219_S | 1.083 | 0.47 |
| 192_R | 195_G | 1.082 | 0.47 |
| 178_L | 181_D | 1.079 | 0.47 |
| 24_L | 318_R | 1.077 | 0.47 |
| 34_Y | 37_A | 1.072 | 0.46 |
| 59_T | 123_I | 1.071 | 0.46 |
| 62_M | 76_D | 1.067 | 0.46 |
| 24_L | 58_E | 1.062 | 0.45 |
| 274_M | 324_M | 1.061 | 0.45 |
| 76_D | 303_E | 1.060 | 0.45 |
| 258_R | 300_R | 1.055 | 0.45 |
| 13_R | 182_R | 1.054 | 0.44 |
| 185_R | 190_R | 1.052 | 0.44 |
| 288_Y | 300_R | 1.051 | 0.44 |
| 297_T | 300_R | 1.045 | 0.44 |
| 132_I | 153_M | 1.044 | 0.43 |
| 96_I | 129_T | 1.042 | 0.43 |
| 37_A | 54_V | 1.038 | 0.43 |
| 124_D | 127_K | 1.038 | 0.43 |
| 126_D | 183_F | 1.036 | 0.43 |
| 38_L | 170_G | 1.034 | 0.43 |
| 315_L | 323_Y | 1.033 | 0.42 |
| 261_E | 300_R | 1.033 | 0.42 |
| 238_Q | 247_K | 1.027 | 0.42 |
| 16_F | 171_I | 1.025 | 0.42 |
| 103_I | 141_K | 1.023 | 0.41 |
| 37_A | 318_R | 1.023 | 0.41 |
| 18_S | 130_Q | 1.022 | 0.41 |
| 150_T | 165_S | 1.019 | 0.41 |
| 297_T | 317_R | 1.019 | 0.41 |
| 33_S | 303_E | 1.018 | 0.41 |
| 34_Y | 315_L | 1.015 | 0.41 |
| 277_E | 316_T | 1.015 | 0.41 |
| 128_M | 202_A | 1.015 | 0.41 |
| 258_R | 290_D | 1.015 | 0.41 |
| 219_S | 222_G | 1.013 | 0.41 |
| 162_L | 176_L | 1.010 | 0.40 |
| 184_Y | 190_R | 1.008 | 0.40 |
| 97_L | 162_L | 1.007 | 0.40 |
| 298_V | 323_Y | 1.006 | 0.40 |
| 290_D | 303_E | 1.005 | 0.40 |
| 76_D | 206_E | 1.005 | 0.40 |
| 239_I | 262_L | 1.005 | 0.40 |
| 171_I | 225_S | 1.003 | 0.40 |
| 16_F | 296_V | 1.002 | 0.39 |
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 | 0.6914 | 100 | 0.584 | Contact Map |
| 2c2aA | 1 | 0.6975 | 100 | 0.597 | Contact Map |
| 2e0aA | 2 | 0.7623 | 100 | 0.613 | Contact Map |
| 4mpcA | 1 | 0.7531 | 100 | 0.623 | Contact Map |
| 1y8oA | 1 | 0.8117 | 100 | 0.623 | Contact Map |
| 4e01A | 1 | 0.7037 | 100 | 0.633 | Contact Map |
| 4ew8A | 2 | 0.7068 | 100 | 0.636 | Contact Map |
| 2q8gA | 1 | 0.7778 | 100 | 0.637 | Contact Map |
| 3a0rA | 1 | 0.6821 | 100 | 0.64 | Contact Map |
| 3jz3A | 2 | 0.4969 | 100 | 0.644 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)