| 1D8DA |
| ID: | 1411607499 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 323 (287) | ||
| Sequences: | 7754 (6204.8) | ||
| Seq/Len: | 27.017 | ||
| Nf(neff/√len): | 366.3 |
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: 27.017).
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 |
| 58_R | 61_R | 4.100 | 1.00 |
| 127_D | 130_Q | 4.046 | 1.00 |
| 161_L | 164_N | 4.034 | 1.00 |
| 92_K | 96_E | 3.841 | 1.00 |
| 237_R | 240_N | 3.356 | 1.00 |
| 195_G | 204_R | 2.494 | 1.00 |
| 50_R | 66_T | 2.359 | 1.00 |
| 119_R | 135_I | 2.277 | 1.00 |
| 153_Q | 169_V | 2.260 | 1.00 |
| 84_R | 101_I | 2.091 | 1.00 |
| 270_E | 275_N | 2.077 | 1.00 |
| 170_D | 186_R | 1.975 | 1.00 |
| 49_F | 65_L | 1.873 | 1.00 |
| 46_Y | 65_L | 1.842 | 1.00 |
| 102_I | 118_R | 1.831 | 1.00 |
| 152_R | 168_Y | 1.803 | 1.00 |
| 210_L | 226_L | 1.786 | 1.00 |
| 67_R | 83_R | 1.782 | 1.00 |
| 166_L | 170_D | 1.781 | 1.00 |
| 83_R | 100_Y | 1.728 | 1.00 |
| 136_A | 152_R | 1.702 | 1.00 |
| 115_W | 134_F | 1.660 | 1.00 |
| 49_F | 53_L | 1.656 | 1.00 |
| 98_M | 102_I | 1.648 | 1.00 |
| 206_V | 210_L | 1.642 | 1.00 |
| 156_I | 164_N | 1.633 | 1.00 |
| 132_L | 136_A | 1.629 | 1.00 |
| 63_F | 67_R | 1.624 | 1.00 |
| 118_R | 134_F | 1.618 | 1.00 |
| 187_H | 209_T | 1.617 | 1.00 |
| 80_W | 100_Y | 1.590 | 1.00 |
| 186_R | 190_I | 1.565 | 1.00 |
| 98_M | 118_R | 1.557 | 1.00 |
| 149_W | 168_Y | 1.548 | 1.00 |
| 209_T | 225_Y | 1.508 | 1.00 |
| 132_L | 152_R | 1.494 | 1.00 |
| 119_R | 138_I | 1.482 | 1.00 |
| 135_I | 151_H | 1.468 | 1.00 |
| 270_E | 282_K | 1.466 | 1.00 |
| 227_K | 242_L | 1.448 | 1.00 |
| 66_T | 82_F | 1.436 | 1.00 |
| 152_R | 156_I | 1.430 | 1.00 |
| 63_F | 83_R | 1.425 | 1.00 |
| 81_H | 117_H | 1.423 | 1.00 |
| 166_L | 189_V | 1.418 | 1.00 |
| 238_Y | 241_L | 1.404 | 0.99 |
| 169_V | 185_Q | 1.404 | 0.99 |
| 60_E | 90_L | 1.398 | 0.99 |
| 166_L | 186_R | 1.387 | 0.99 |
| 132_L | 155_V | 1.377 | 0.99 |
| 226_L | 230_L | 1.364 | 0.99 |
| 183_W | 208_Y | 1.350 | 0.99 |
| 172_L | 182_V | 1.331 | 0.99 |
| 118_R | 122_V | 1.323 | 0.99 |
| 186_R | 208_Y | 1.321 | 0.99 |
| 122_V | 130_Q | 1.315 | 0.99 |
| 171_Q | 174_K | 1.305 | 0.99 |
| 63_F | 86_L | 1.296 | 0.99 |
| 47_D | 82_F | 1.284 | 0.99 |
| 83_R | 87_L | 1.276 | 0.99 |
| 234_G | 238_Y | 1.276 | 0.99 |
| 211_E | 215_L | 1.265 | 0.99 |
| 122_V | 127_D | 1.261 | 0.99 |
| 295_D | 298_R | 1.254 | 0.99 |
| 211_E | 214_K | 1.254 | 0.99 |
| 101_I | 117_H | 1.252 | 0.99 |
| 130_Q | 133_E | 1.245 | 0.98 |
| 142_D | 145_N | 1.234 | 0.98 |
| 150_Q | 182_V | 1.231 | 0.98 |
| 53_L | 61_R | 1.226 | 0.98 |
| 190_I | 195_G | 1.225 | 0.98 |
| 137_D | 140_N | 1.225 | 0.98 |
| 98_M | 121_L | 1.222 | 0.98 |
| 91_Q | 94_L | 1.218 | 0.98 |
| 68_D | 71_E | 1.213 | 0.98 |
| 206_V | 226_L | 1.205 | 0.98 |
| 289_I | 293_E | 1.204 | 0.98 |
| 305_I | 309_L | 1.203 | 0.98 |
| 53_L | 58_R | 1.199 | 0.98 |
| 63_F | 87_L | 1.198 | 0.98 |
| 105_I | 115_W | 1.194 | 0.98 |
| 164_N | 167_Q | 1.188 | 0.98 |
| 52_V | 56_D | 1.187 | 0.98 |
| 223_W | 244_Q | 1.180 | 0.98 |
| 204_R | 207_Q | 1.177 | 0.98 |
| 184_N | 225_Y | 1.173 | 0.98 |
| 138_I | 148_A | 1.166 | 0.97 |
| 150_Q | 185_Q | 1.165 | 0.97 |
| 87_L | 96_E | 1.161 | 0.97 |
| 50_R | 65_L | 1.156 | 0.97 |
| 259_A | 262_V | 1.153 | 0.97 |
| 80_W | 149_W | 1.152 | 0.97 |
| 129_S | 159_F | 1.151 | 0.97 |
| 84_R | 104_I | 1.150 | 0.97 |
| 116_H | 151_H | 1.144 | 0.97 |
| 95_Q | 163_D | 1.143 | 0.97 |
| 261_L | 265_Y | 1.139 | 0.97 |
| 98_M | 122_V | 1.138 | 0.97 |
| 185_Q | 225_Y | 1.133 | 0.97 |
| 216_V | 219_N | 1.119 | 0.96 |
| 188_F | 225_Y | 1.115 | 0.96 |
| 154_W | 185_Q | 1.114 | 0.96 |
| 36_I | 46_Y | 1.108 | 0.96 |
| 168_Y | 208_Y | 1.107 | 0.96 |
| 108_Q | 111_N | 1.107 | 0.96 |
| 102_I | 130_Q | 1.106 | 0.96 |
| 244_Q | 247_D | 1.102 | 0.96 |
| 269_L | 273_C | 1.101 | 0.96 |
| 47_D | 79_V | 1.100 | 0.96 |
| 252_H | 255_P | 1.100 | 0.96 |
| 53_L | 65_L | 1.099 | 0.96 |
| 206_V | 229_I | 1.097 | 0.96 |
| 70_I | 79_V | 1.094 | 0.96 |
| 61_R | 64_K | 1.086 | 0.96 |
| 265_Y | 270_E | 1.079 | 0.95 |
| 284_L | 288_E | 1.078 | 0.95 |
| 87_L | 100_Y | 1.076 | 0.95 |
| 86_L | 90_L | 1.075 | 0.95 |
| 206_V | 230_L | 1.075 | 0.95 |
| 112_Y | 138_I | 1.072 | 0.95 |
| 132_L | 156_I | 1.070 | 0.95 |
| 122_V | 134_F | 1.066 | 0.95 |
| 95_Q | 125_L | 1.066 | 0.95 |
| 89_S | 158_E | 1.064 | 0.95 |
| 171_Q | 175_E | 1.063 | 0.95 |
| 63_F | 90_L | 1.062 | 0.95 |
| 163_D | 193_T | 1.059 | 0.95 |
| 292_K | 302_W | 1.048 | 0.94 |
| 166_L | 193_T | 1.041 | 0.94 |
| 50_R | 69_A | 1.039 | 0.94 |
| 224_N | 260_F | 1.035 | 0.94 |
| 98_M | 125_L | 1.031 | 0.94 |
| 115_W | 137_D | 1.030 | 0.94 |
| 282_K | 285_E | 1.023 | 0.93 |
| 140_N | 174_K | 1.023 | 0.93 |
| 132_L | 159_F | 1.016 | 0.93 |
| 166_L | 190_I | 1.013 | 0.93 |
| 101_I | 169_V | 1.013 | 0.93 |
| 183_W | 223_W | 1.013 | 0.93 |
| 173_L | 183_W | 1.006 | 0.93 |
| 99_N | 133_E | 1.003 | 0.93 |
| 96_E | 99_N | 1.002 | 0.92 |
| 242_L | 246_L | 1.001 | 0.92 |
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 | |
| 2h6fA | 1 | 0.9659 | 100 | 0.281 | Contact Map |
| 4l9pA | 1 | 0.9133 | 100 | 0.283 | Contact Map |
| 3iegA | 2 | 0.9195 | 100 | 0.307 | Contact Map |
| 3q7aA | 1 | 0.8947 | 100 | 0.315 | Contact Map |
| 2y4tA | 3 | 0.9009 | 100 | 0.323 | Contact Map |
| 3fp2A | 1 | 0.9133 | 100 | 0.345 | Contact Map |
| 1w3bA | 2 | 0.935 | 100 | 0.352 | Contact Map |
| 2xpiA | 2 | 0.9381 | 100 | 0.357 | Contact Map |
| 3draA | 1 | 0.8762 | 100 | 0.363 | Contact Map |
| 1fchA | 2 | 0.8452 | 100 | 0.364 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)