| Spo0J |
| ID: | 1487683062 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 282 (275) | ||
| Sequences: | 3396 (2211.8) | ||
| Seq/Len: | 12.349 | ||
| Nf(neff/√len): | 133.4 |
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: 12.349).
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 |
| 25_E | 91_T | 4.579 | 1.00 |
| 197_K | 201_E | 3.929 | 1.00 |
| 168_L | 195_V | 3.861 | 1.00 |
| 148_S | 151_H | 3.842 | 1.00 |
| 198_V | 208_L | 3.727 | 1.00 |
| 128_D | 132_K | 3.595 | 1.00 |
| 138_Q | 153_A | 3.249 | 1.00 |
| 32_R | 71_G | 3.200 | 1.00 |
| 74_I | 81_F | 3.177 | 1.00 |
| 51_K | 86_L | 2.775 | 1.00 |
| 129_S | 133_H | 2.758 | 1.00 |
| 31_L | 74_I | 2.675 | 1.00 |
| 63_L | 92_V | 2.634 | 1.00 |
| 203_L | 211_L | 2.587 | 1.00 |
| 59_I | 84_A | 2.509 | 1.00 |
| 27_K | 30_D | 2.487 | 1.00 |
| 48_A | 52_E | 2.477 | 1.00 |
| 121_L | 166_Q | 2.469 | 1.00 |
| 125_Q | 166_Q | 2.359 | 1.00 |
| 26_I | 94_A | 2.324 | 1.00 |
| 63_L | 74_I | 2.285 | 1.00 |
| 207_Q | 210_Q | 2.257 | 1.00 |
| 48_A | 86_L | 2.225 | 1.00 |
| 44_D | 86_L | 2.176 | 1.00 |
| 272_R | 276_L | 2.173 | 1.00 |
| 131_L | 141_L | 2.159 | 1.00 |
| 167_Q | 171_E | 2.103 | 1.00 |
| 168_L | 199_I | 2.077 | 1.00 |
| 28_I | 81_F | 2.055 | 1.00 |
| 60_L | 64_I | 2.054 | 1.00 |
| 194_L | 211_L | 2.043 | 1.00 |
| 47_L | 86_L | 2.035 | 1.00 |
| 26_I | 65_V | 2.032 | 1.00 |
| 230_K | 238_E | 2.024 | 1.00 |
| 178_H | 205_V | 1.997 | 1.00 |
| 81_F | 85_K | 1.938 | 1.00 |
| 43_D | 46_A | 1.925 | 1.00 |
| 140_Q | 143_K | 1.925 | 1.00 |
| 46_A | 116_E | 1.904 | 1.00 |
| 99_L | 107_I | 1.889 | 1.00 |
| 66_R | 73_D | 1.852 | 1.00 |
| 269_D | 272_R | 1.852 | 1.00 |
| 65_V | 94_A | 1.842 | 1.00 |
| 30_D | 71_G | 1.815 | 1.00 |
| 165_I | 195_V | 1.805 | 1.00 |
| 44_D | 48_A | 1.761 | 1.00 |
| 75_V | 99_L | 1.730 | 1.00 |
| 150_P | 153_A | 1.728 | 1.00 |
| 139_E | 143_K | 1.706 | 1.00 |
| 32_R | 73_D | 1.687 | 1.00 |
| 155_H | 176_M | 1.677 | 1.00 |
| 169_I | 179_G | 1.660 | 1.00 |
| 267_N | 271_D | 1.639 | 1.00 |
| 162_P | 191_L | 1.613 | 1.00 |
| 185_L | 194_L | 1.600 | 1.00 |
| 52_E | 55_L | 1.594 | 1.00 |
| 84_A | 89_L | 1.577 | 1.00 |
| 195_V | 199_I | 1.567 | 1.00 |
| 181_T | 208_L | 1.556 | 1.00 |
| 181_T | 205_V | 1.524 | 1.00 |
| 31_L | 65_V | 1.502 | 1.00 |
| 119_S | 170_A | 1.494 | 1.00 |
| 66_R | 101_E | 1.492 | 1.00 |
| 240_Y | 278_S | 1.491 | 1.00 |
| 27_K | 91_T | 1.480 | 1.00 |
| 168_L | 173_T | 1.473 | 1.00 |
| 178_H | 181_T | 1.456 | 1.00 |
| 47_L | 51_K | 1.438 | 1.00 |
| 63_L | 94_A | 1.422 | 1.00 |
| 100_S | 103_L | 1.413 | 1.00 |
| 271_D | 275_E | 1.411 | 1.00 |
| 125_Q | 170_A | 1.406 | 0.99 |
| 84_A | 87_A | 1.403 | 0.99 |
| 38_P | 108_A | 1.383 | 0.99 |
| 197_K | 211_L | 1.342 | 0.99 |
| 190_K | 193_P | 1.339 | 0.99 |
| 196_Q | 200_A | 1.334 | 0.99 |
| 204_N | 207_Q | 1.333 | 0.99 |
| 52_E | 56_Q | 1.322 | 0.99 |
| 265_F | 269_D | 1.317 | 0.99 |
| 164_N | 196_Q | 1.297 | 0.99 |
| 203_L | 208_L | 1.280 | 0.99 |
| 252_K | 261_E | 1.274 | 0.99 |
| 266_S | 269_D | 1.267 | 0.99 |
| 163_E | 166_Q | 1.266 | 0.99 |
| 66_R | 104_M | 1.264 | 0.99 |
| 59_I | 93_P | 1.261 | 0.99 |
| 141_L | 152_I | 1.247 | 0.99 |
| 67_K | 70_K | 1.234 | 0.98 |
| 176_M | 180_R | 1.231 | 0.98 |
| 59_I | 92_V | 1.229 | 0.98 |
| 177_G | 206_R | 1.225 | 0.98 |
| 54_V | 84_A | 1.213 | 0.98 |
| 127_Y | 145_L | 1.211 | 0.98 |
| 206_R | 209_E | 1.203 | 0.98 |
| 198_V | 203_L | 1.203 | 0.98 |
| 34_N | 104_M | 1.200 | 0.98 |
| 54_V | 59_I | 1.196 | 0.98 |
| 31_L | 92_V | 1.187 | 0.98 |
| 123_E | 147_K | 1.181 | 0.98 |
| 208_L | 212_I | 1.176 | 0.98 |
| 48_A | 51_K | 1.163 | 0.97 |
| 106_E | 144_R | 1.158 | 0.97 |
| 167_Q | 170_A | 1.157 | 0.97 |
| 203_L | 207_Q | 1.151 | 0.97 |
| 187_N | 190_K | 1.150 | 0.97 |
| 210_Q | 213_Q | 1.127 | 0.97 |
| 56_Q | 143_K | 1.126 | 0.97 |
| 190_K | 215_L | 1.121 | 0.97 |
| 131_L | 138_Q | 1.114 | 0.96 |
| 64_I | 76_A | 1.109 | 0.96 |
| 245_F | 262_I | 1.107 | 0.96 |
| 233_V | 236_E | 1.103 | 0.96 |
| 174_L | 195_V | 1.099 | 0.96 |
| 165_I | 191_L | 1.095 | 0.96 |
| 131_L | 153_A | 1.084 | 0.96 |
| 168_L | 174_L | 1.075 | 0.95 |
| 29_A | 85_K | 1.063 | 0.95 |
| 194_L | 215_L | 1.059 | 0.95 |
| 253_R | 264_F | 1.057 | 0.95 |
| 123_E | 155_H | 1.047 | 0.94 |
| 184_G | 216_N | 1.034 | 0.94 |
| 8_G | 12_L | 1.025 | 0.93 |
| 236_E | 240_Y | 1.018 | 0.93 |
| 33_P | 81_F | 1.013 | 0.93 |
| 163_E | 167_Q | 1.012 | 0.93 |
| 102_A | 106_E | 1.009 | 0.93 |
| 194_L | 208_L | 1.006 | 0.93 |
| 59_I | 63_L | 1.005 | 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 | |
| 4umkA | 4 | 0 | 100 | 0.326 | Contact Map |
| 1vz0A | 8 | 0.6809 | 100 | 0.334 | Contact Map |
| 1r71A | 4 | 0.3936 | 100 | 0.642 | Contact Map |
| 3mkyB | 2 | 0.3865 | 100 | 0.65 | Contact Map |
| 1vk1A | 1 | 0.6879 | 99.9 | 0.683 | Contact Map |
| 1yzsA | 1 | 0.3865 | 99.9 | 0.7 | Contact Map |
| 1xw3A | 1 | 0.3511 | 99.9 | 0.7 | Contact Map |
| 1zx4A | 2 | 0.5745 | 99.2 | 0.828 | Contact Map |
| 2hwjA | 6 | 0.6312 | 95.8 | 0.916 | Contact Map |
| 3vwbA | 1 | 0.4078 | 93.6 | 0.925 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)