| BPGM-2 |
| ID: | 1467839906 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 258 (228) | ||
| Sequences: | 2292 (1219.2) | ||
| Seq/Len: | 10.053 | ||
| Nf(neff/√len): | 80.7 |
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: 10.053).
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 |
| 8_L | 69_I | 3.887 | 1.00 |
| 54_V | 66_A | 3.855 | 1.00 |
| 12_E | 32_E | 3.727 | 1.00 |
| 124_P | 154_S | 3.258 | 1.00 |
| 196_K | 203_D | 2.793 | 1.00 |
| 53_L | 81_E | 2.713 | 1.00 |
| 118_Y | 161_L | 2.668 | 1.00 |
| 28_K | 64_H | 2.519 | 1.00 |
| 195_L | 211_L | 2.502 | 1.00 |
| 199_E | 219_L | 2.463 | 1.00 |
| 121_T | 159_D | 2.239 | 1.00 |
| 6_I | 51_F | 2.232 | 1.00 |
| 4_K | 220_E | 2.210 | 1.00 |
| 202_S | 205_D | 2.203 | 1.00 |
| 14_A | 18_E | 2.139 | 1.00 |
| 201_I | 205_D | 2.139 | 1.00 |
| 42_K | 72_E | 2.099 | 1.00 |
| 31_S | 34_M | 2.081 | 1.00 |
| 147_P | 150_Q | 2.065 | 1.00 |
| 156_S | 159_D | 2.045 | 1.00 |
| 67_W | 76_E | 2.015 | 1.00 |
| 125_I | 129_H | 1.989 | 1.00 |
| 55_F | 175_E | 1.989 | 1.00 |
| 38_R | 72_E | 1.973 | 1.00 |
| 222_D | 226_R | 1.966 | 1.00 |
| 158_K | 162_E | 1.933 | 1.00 |
| 97_L | 102_M | 1.913 | 1.00 |
| 100_E | 103_A | 1.901 | 1.00 |
| 140_R | 143_V | 1.852 | 1.00 |
| 143_V | 146_V | 1.852 | 1.00 |
| 55_F | 167_Y | 1.833 | 1.00 |
| 39_N | 42_K | 1.828 | 1.00 |
| 97_L | 105_N | 1.827 | 1.00 |
| 119_N | 158_K | 1.792 | 1.00 |
| 186_A | 190_S | 1.778 | 1.00 |
| 35_E | 38_R | 1.762 | 1.00 |
| 112_R | 208_N | 1.743 | 1.00 |
| 34_M | 64_H | 1.725 | 1.00 |
| 28_K | 60_N | 1.725 | 1.00 |
| 201_I | 206_I | 1.714 | 1.00 |
| 44_L | 49_F | 1.695 | 1.00 |
| 53_L | 182_I | 1.684 | 1.00 |
| 173_A | 225_L | 1.677 | 1.00 |
| 54_V | 78_V | 1.662 | 1.00 |
| 64_H | 71_E | 1.652 | 1.00 |
| 175_E | 178_R | 1.652 | 1.00 |
| 125_I | 131_Y | 1.650 | 1.00 |
| 113_L | 117_S | 1.642 | 1.00 |
| 34_M | 68_L | 1.638 | 1.00 |
| 103_A | 111_V | 1.622 | 1.00 |
| 127_E | 153_R | 1.618 | 1.00 |
| 132_Y | 153_R | 1.566 | 1.00 |
| 25_V | 131_Y | 1.557 | 1.00 |
| 165_L | 197_H | 1.546 | 1.00 |
| 38_R | 68_L | 1.544 | 1.00 |
| 22_C | 27_Q | 1.526 | 1.00 |
| 12_E | 30_N | 1.516 | 1.00 |
| 159_D | 162_E | 1.515 | 1.00 |
| 121_T | 124_P | 1.506 | 1.00 |
| 36_E | 213_T | 1.503 | 1.00 |
| 42_K | 46_A | 1.484 | 1.00 |
| 41_G | 72_E | 1.478 | 1.00 |
| 49_F | 181_T | 1.476 | 1.00 |
| 67_W | 80_V | 1.467 | 1.00 |
| 64_H | 76_E | 1.454 | 1.00 |
| 44_L | 73_L | 1.415 | 1.00 |
| 172_I | 184_I | 1.407 | 0.99 |
| 171_R | 175_E | 1.398 | 0.99 |
| 12_E | 17_K | 1.392 | 0.99 |
| 127_E | 148_L | 1.380 | 0.99 |
| 141_Y | 144_C | 1.370 | 0.99 |
| 34_M | 38_R | 1.363 | 0.99 |
| 142_K | 146_V | 1.349 | 0.99 |
| 221_L | 225_L | 1.316 | 0.99 |
| 81_E | 171_R | 1.303 | 0.99 |
| 74_G | 77_W | 1.297 | 0.99 |
| 127_E | 132_Y | 1.279 | 0.99 |
| 133_Q | 151_L | 1.279 | 0.99 |
| 51_F | 181_T | 1.238 | 0.98 |
| 146_V | 151_L | 1.238 | 0.98 |
| 13_G | 16_N | 1.236 | 0.98 |
| 143_V | 148_L | 1.236 | 0.98 |
| 63_I | 77_W | 1.228 | 0.98 |
| 60_N | 74_G | 1.224 | 0.98 |
| 64_H | 67_W | 1.213 | 0.98 |
| 25_V | 129_H | 1.179 | 0.98 |
| 37_A | 65_T | 1.171 | 0.98 |
| 50_E | 181_T | 1.150 | 0.97 |
| 102_M | 106_H | 1.135 | 0.97 |
| 44_L | 69_I | 1.125 | 0.97 |
| 144_C | 147_P | 1.118 | 0.96 |
| 128_S | 132_Y | 1.113 | 0.96 |
| 55_F | 171_R | 1.102 | 0.96 |
| 35_E | 39_N | 1.097 | 0.96 |
| 71_E | 76_E | 1.082 | 0.96 |
| 143_V | 147_P | 1.073 | 0.95 |
| 32_E | 35_E | 1.056 | 0.95 |
| 145_D | 148_L | 1.030 | 0.94 |
| 102_M | 111_V | 1.026 | 0.94 |
| 58_V | 79_P | 1.022 | 0.93 |
| 155_E | 163_R | 1.022 | 0.93 |
| 144_C | 148_L | 1.020 | 0.93 |
| 19_N | 98_N | 1.017 | 0.93 |
| 156_S | 161_L | 1.009 | 0.93 |
| 31_S | 35_E | 1.009 | 0.93 |
| 132_Y | 148_L | 1.005 | 0.93 |
| 164_L | 193_A | 1.004 | 0.93 |
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 | |
| 2hhjA | 2 | 0.9845 | 100 | 0.189 | Contact Map |
| 4odiA | 4 | 0.9419 | 100 | 0.229 | Contact Map |
| 1riiA | 4 | 0.9341 | 100 | 0.229 | Contact Map |
| 3d8hA | 2 | 0.8992 | 100 | 0.265 | Contact Map |
| 3kkkA | 4 | 0.8915 | 100 | 0.27 | Contact Map |
| 3gp3A | 4 | 0.8915 | 100 | 0.272 | Contact Map |
| 4gpzA | 2 | 0.9302 | 100 | 0.276 | Contact Map |
| 1e58A | 1 | 0.9535 | 100 | 0.278 | Contact Map |
| 4embA | 4 | 0.9496 | 100 | 0.294 | Contact Map |
| 1qhfA | 2 | 0.9302 | 100 | 0.295 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)