| 1268 |
| ID: | 1470426426 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 173 (155) | ||
| Sequences: | 2058 (1440) | ||
| Seq/Len: | 13.277 | ||
| Nf(neff/√len): | 115.7 |
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: 13.277).
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 |
| 111_T | 133_T | 4.050 | 1.00 |
| 35_V | 78_A | 3.299 | 1.00 |
| 75_V | 89_D | 3.265 | 1.00 |
| 32_T | 54_T | 2.823 | 1.00 |
| 78_A | 81_V | 2.487 | 1.00 |
| 137_V | 165_S | 2.218 | 1.00 |
| 58_V | 86_S | 2.149 | 1.00 |
| 35_V | 59_V | 2.010 | 1.00 |
| 65_V | 91_L | 1.967 | 1.00 |
| 129_V | 144_V | 1.916 | 1.00 |
| 154_E | 168_N | 1.858 | 1.00 |
| 67_S | 70_Q | 1.853 | 1.00 |
| 53_K | 62_S | 1.847 | 1.00 |
| 138_V | 163_V | 1.837 | 1.00 |
| 31_I | 54_T | 1.829 | 1.00 |
| 114_I | 138_V | 1.819 | 1.00 |
| 163_V | 166_V | 1.760 | 1.00 |
| 61_L | 74_A | 1.719 | 1.00 |
| 75_V | 79_K | 1.626 | 1.00 |
| 114_I | 157_A | 1.601 | 1.00 |
| 66_E | 70_Q | 1.576 | 1.00 |
| 50_I | 61_L | 1.544 | 1.00 |
| 61_L | 78_A | 1.537 | 1.00 |
| 59_V | 84_V | 1.505 | 1.00 |
| 68_Q | 72_E | 1.493 | 1.00 |
| 110_T | 133_T | 1.491 | 1.00 |
| 109_A | 113_E | 1.485 | 1.00 |
| 49_D | 64_F | 1.476 | 1.00 |
| 121_D | 152_R | 1.429 | 1.00 |
| 141_S | 169_D | 1.414 | 1.00 |
| 144_V | 170_L | 1.392 | 0.99 |
| 150_S | 154_E | 1.390 | 0.99 |
| 39_L | 74_A | 1.389 | 0.99 |
| 23_G | 27_D | 1.375 | 0.99 |
| 35_V | 81_V | 1.369 | 0.99 |
| 112_S | 116_A | 1.367 | 0.99 |
| 130_K | 141_S | 1.365 | 0.99 |
| 58_V | 88_S | 1.344 | 0.99 |
| 118_L | 124_V | 1.342 | 0.99 |
| 64_F | 92_H | 1.326 | 0.99 |
| 68_Q | 71_A | 1.323 | 0.99 |
| 111_T | 115_K | 1.310 | 0.99 |
| 136_G | 164_K | 1.298 | 0.99 |
| 64_F | 94_R | 1.288 | 0.99 |
| 153_A | 157_A | 1.282 | 0.99 |
| 119_L | 126_S | 1.274 | 0.99 |
| 157_A | 166_V | 1.272 | 0.99 |
| 139_Q | 167_K | 1.268 | 0.99 |
| 147_Q | 151_D | 1.264 | 0.99 |
| 36_K | 52_V | 1.251 | 0.99 |
| 30_A | 34_K | 1.235 | 0.98 |
| 28_D | 57_K | 1.232 | 0.98 |
| 42_H | 73_E | 1.232 | 0.98 |
| 54_T | 59_V | 1.219 | 0.98 |
| 35_V | 39_L | 1.205 | 0.98 |
| 140_L | 153_A | 1.192 | 0.98 |
| 31_I | 83_G | 1.185 | 0.98 |
| 31_I | 59_V | 1.183 | 0.98 |
| 71_A | 93_V | 1.179 | 0.98 |
| 26_M | 34_K | 1.160 | 0.97 |
| 117_K | 156_I | 1.152 | 0.97 |
| 132_E | 141_S | 1.124 | 0.97 |
| 31_I | 84_V | 1.119 | 0.96 |
| 60_T | 139_Q | 1.109 | 0.96 |
| 137_V | 167_K | 1.097 | 0.96 |
| 124_V | 152_R | 1.094 | 0.96 |
| 51_S | 62_S | 1.089 | 0.96 |
| 50_I | 91_L | 1.085 | 0.96 |
| 27_D | 30_A | 1.084 | 0.96 |
| 109_A | 112_S | 1.080 | 0.95 |
| 99_G | 104_Y | 1.062 | 0.95 |
| 33_A | 37_A | 1.061 | 0.95 |
| 110_T | 138_V | 1.061 | 0.95 |
| 157_A | 160_V | 1.059 | 0.95 |
| 49_D | 99_G | 1.051 | 0.94 |
| 84_V | 87_V | 1.049 | 0.94 |
| 73_E | 77_V | 1.047 | 0.94 |
| 92_H | 137_V | 1.045 | 0.94 |
| 74_A | 77_V | 1.041 | 0.94 |
| 38_A | 77_V | 1.039 | 0.94 |
| 32_T | 36_K | 1.016 | 0.93 |
| 26_M | 30_A | 1.014 | 0.93 |
| 145_D | 149_Q | 1.011 | 0.93 |
| 124_V | 153_A | 1.011 | 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 | |
| 2kgsA | 1 | 0.7052 | 99.9 | 0.482 | Contact Map |
| 4alzA | 1 | 0.7225 | 99.8 | 0.494 | Contact Map |
| 2l26A | 1 | 0.6936 | 99 | 0.704 | Contact Map |
| 4qq0A | 1 | 0 | 97.8 | 0.794 | Contact Map |
| 1uwdA | 1 | 0.4971 | 50.9 | 0.91 | Contact Map |
| 3cq1A | 1 | 0.5318 | 31.7 | 0.92 | Contact Map |
| 3lnoA | 6 | 0.5318 | 29.9 | 0.921 | Contact Map |
| 3bypA | 2 | 0.1676 | 17.7 | 0.929 | Contact Map |
| 2j58A | 8 | 0.9538 | 9.9 | 0.937 | Contact Map |
| 3ux2A | 1 | 0.6474 | 9.1 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)