| MORE |
| ID: | 1393596119 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 324 (324) | ||
| Sequences: | 462 (324.8) | ||
| Seq/Len: | 1.426 | ||
| Nf(neff/√len): | 18.0 |
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: 1.426).
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 | 3.728 | 1.00 |
| 308_T | 311_R | 2.891 | 1.00 |
| 308_T | 312_P | 2.849 | 1.00 |
| 217_A | 227_F | 2.243 | 0.99 |
| 64_R | 126_D | 2.211 | 0.99 |
| 306_E | 312_P | 2.122 | 0.99 |
| 16_F | 183_F | 2.106 | 0.99 |
| 121_I | 231_L | 2.074 | 0.98 |
| 70_L | 197_T | 2.057 | 0.98 |
| 131_V | 207_I | 2.032 | 0.98 |
| 35_L | 55_S | 2.025 | 0.98 |
| 149_V | 164_I | 2.023 | 0.98 |
| 34_Y | 54_V | 2.010 | 0.98 |
| 180_F | 215_I | 2.007 | 0.98 |
| 34_Y | 300_R | 2.005 | 0.98 |
| 239_I | 267_A | 1.949 | 0.97 |
| 172_P | 186_V | 1.922 | 0.97 |
| 265_H | 279_L | 1.910 | 0.97 |
| 135_I | 229_I | 1.908 | 0.97 |
| 143_S | 167_Q | 1.865 | 0.96 |
| 220_E | 223_E | 1.862 | 0.96 |
| 111_I | 151_V | 1.817 | 0.95 |
| 165_S | 226_T | 1.674 | 0.92 |
| 75_I | 206_E | 1.648 | 0.91 |
| 31_V | 55_S | 1.644 | 0.91 |
| 303_E | 323_Y | 1.638 | 0.91 |
| 307_D | 311_R | 1.617 | 0.90 |
| 17_V | 182_R | 1.589 | 0.89 |
| 258_R | 297_T | 1.552 | 0.88 |
| 208_V | 229_I | 1.543 | 0.87 |
| 69_L | 290_D | 1.527 | 0.86 |
| 306_E | 309_P | 1.520 | 0.86 |
| 89_F | 160_L | 1.501 | 0.85 |
| 132_I | 164_I | 1.475 | 0.84 |
| 61_R | 191_S | 1.455 | 0.83 |
| 69_L | 211_H | 1.437 | 0.82 |
| 246_A | 253_V | 1.422 | 0.81 |
| 236_D | 249_R | 1.396 | 0.79 |
| 277_E | 281_E | 1.383 | 0.78 |
| 41_G | 48_A | 1.382 | 0.78 |
| 142_Y | 185_R | 1.380 | 0.78 |
| 298_V | 305_I | 1.374 | 0.77 |
| 19_N | 29_T | 1.359 | 0.76 |
| 303_E | 317_R | 1.358 | 0.76 |
| 171_I | 179_I | 1.346 | 0.75 |
| 317_R | 323_Y | 1.344 | 0.75 |
| 33_S | 54_V | 1.311 | 0.73 |
| 162_L | 229_I | 1.302 | 0.72 |
| 143_S | 147_G | 1.283 | 0.70 |
| 34_Y | 62_M | 1.280 | 0.70 |
| 123_I | 128_M | 1.279 | 0.70 |
| 188_K | 192_R | 1.270 | 0.69 |
| 30_S | 66_I | 1.264 | 0.69 |
| 96_I | 136_L | 1.259 | 0.68 |
| 18_S | 181_D | 1.258 | 0.68 |
| 273_V | 300_R | 1.248 | 0.67 |
| 270_T | 274_M | 1.240 | 0.66 |
| 307_D | 312_P | 1.239 | 0.66 |
| 18_S | 145_D | 1.233 | 0.66 |
| 283_V | 300_R | 1.228 | 0.65 |
| 245_V | 252_E | 1.222 | 0.65 |
| 283_V | 303_E | 1.218 | 0.64 |
| 3_A | 7_E | 1.216 | 0.64 |
| 96_I | 176_L | 1.213 | 0.64 |
| 236_D | 313_Y | 1.210 | 0.64 |
| 34_Y | 318_R | 1.208 | 0.64 |
| 276_R | 295_D | 1.208 | 0.64 |
| 269_H | 272_Q | 1.207 | 0.63 |
| 219_S | 223_E | 1.201 | 0.63 |
| 306_E | 310_S | 1.197 | 0.62 |
| 292_R | 295_D | 1.187 | 0.62 |
| 163_S | 226_T | 1.175 | 0.60 |
| 17_V | 142_Y | 1.171 | 0.60 |
| 39_D | 324_M | 1.170 | 0.60 |
| 33_S | 62_M | 1.169 | 0.60 |
| 258_R | 283_V | 1.161 | 0.59 |
| 185_R | 190_R | 1.161 | 0.59 |
| 124_D | 127_K | 1.159 | 0.59 |
| 290_D | 303_E | 1.157 | 0.59 |
| 178_L | 181_D | 1.157 | 0.59 |
| 204_A | 215_I | 1.155 | 0.58 |
| 257_H | 261_E | 1.154 | 0.58 |
| 35_L | 56_L | 1.153 | 0.58 |
| 135_I | 164_I | 1.153 | 0.58 |
| 274_M | 324_M | 1.151 | 0.58 |
| 205_K | 209_K | 1.150 | 0.58 |
| 208_V | 237_L | 1.148 | 0.58 |
| 239_I | 246_A | 1.146 | 0.57 |
| 276_R | 292_R | 1.146 | 0.57 |
| 290_D | 300_R | 1.144 | 0.57 |
| 172_P | 188_K | 1.140 | 0.57 |
| 54_V | 318_R | 1.130 | 0.56 |
| 69_L | 202_A | 1.129 | 0.56 |
| 192_R | 195_G | 1.126 | 0.55 |
| 76_D | 206_E | 1.122 | 0.55 |
| 146_G | 202_A | 1.120 | 0.55 |
| 235_G | 298_V | 1.117 | 0.55 |
| 17_V | 72_L | 1.116 | 0.54 |
| 76_D | 303_E | 1.115 | 0.54 |
| 150_T | 165_S | 1.115 | 0.54 |
| 13_R | 182_R | 1.112 | 0.54 |
| 37_A | 54_V | 1.103 | 0.53 |
| 257_H | 300_R | 1.101 | 0.53 |
| 33_S | 303_E | 1.096 | 0.52 |
| 177_P | 191_S | 1.095 | 0.52 |
| 293_T | 297_T | 1.093 | 0.52 |
| 237_L | 246_A | 1.088 | 0.52 |
| 219_S | 222_G | 1.087 | 0.52 |
| 24_L | 318_R | 1.086 | 0.51 |
| 66_I | 265_H | 1.085 | 0.51 |
| 184_Y | 190_R | 1.085 | 0.51 |
| 238_Q | 247_K | 1.084 | 0.51 |
| 255_L | 301_L | 1.077 | 0.51 |
| 206_E | 297_T | 1.071 | 0.50 |
| 258_R | 284_W | 1.069 | 0.50 |
| 208_V | 213_G | 1.065 | 0.49 |
| 176_L | 217_A | 1.056 | 0.48 |
| 172_P | 320_V | 1.055 | 0.48 |
| 213_G | 231_L | 1.054 | 0.48 |
| 125_T | 314_I | 1.053 | 0.48 |
| 173_K | 219_S | 1.053 | 0.48 |
| 298_V | 323_Y | 1.051 | 0.48 |
| 132_I | 136_L | 1.051 | 0.48 |
| 215_I | 266_L | 1.049 | 0.48 |
| 258_R | 300_R | 1.047 | 0.47 |
| 277_E | 316_T | 1.047 | 0.47 |
| 24_L | 58_E | 1.046 | 0.47 |
| 66_I | 227_F | 1.046 | 0.47 |
| 33_S | 206_E | 1.044 | 0.47 |
| 126_D | 183_F | 1.037 | 0.46 |
| 160_L | 233_Y | 1.037 | 0.46 |
| 109_Y | 149_V | 1.036 | 0.46 |
| 280_L | 285_G | 1.034 | 0.46 |
| 297_T | 317_R | 1.028 | 0.46 |
| 16_F | 171_I | 1.027 | 0.45 |
| 284_W | 288_Y | 1.027 | 0.45 |
| 139_A | 168_G | 1.026 | 0.45 |
| 280_L | 294_V | 1.026 | 0.45 |
| 34_Y | 315_L | 1.024 | 0.45 |
| 34_Y | 37_A | 1.024 | 0.45 |
| 237_L | 263_L | 1.023 | 0.45 |
| 288_Y | 300_R | 1.022 | 0.45 |
| 16_F | 296_V | 1.018 | 0.45 |
| 239_I | 244_F | 1.017 | 0.44 |
| 97_L | 162_L | 1.016 | 0.44 |
| 171_I | 219_S | 1.015 | 0.44 |
| 258_R | 291_V | 1.014 | 0.44 |
| 171_I | 225_S | 1.012 | 0.44 |
| 221_E | 233_Y | 1.009 | 0.44 |
| 142_Y | 207_I | 1.009 | 0.44 |
| 12_E | 37_A | 1.008 | 0.43 |
| 132_I | 153_M | 1.008 | 0.43 |
| 58_E | 185_R | 1.004 | 0.43 |
| 34_Y | 265_H | 1.003 | 0.43 |
| 14_R | 234_I | 1.003 | 0.43 |
| 54_V | 62_M | 1.002 | 0.43 |
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 | 0.582 | Contact Map |
| 2c2aA | 1 | 0.6975 | 100 | 0.595 | Contact Map |
| 2e0aA | 2 | 0.7623 | 100 | 0.611 | Contact Map |
| 4mpcA | 1 | 0.7531 | 100 | 0.62 | Contact Map |
| 1y8oA | 1 | 0.8117 | 100 | 0.621 | Contact Map |
| 4e01A | 1 | 0.7037 | 100 | 0.632 | Contact Map |
| 4ew8A | 2 | 0.7068 | 100 | 0.634 | Contact Map |
| 2q8gA | 1 | 0.7778 | 100 | 0.635 | Contact Map |
| 3a0rA | 1 | 0.6821 | 100 | 0.637 | Contact Map |
| 3jz3A | 2 | 0.4969 | 100 | 0.642 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)