| vko |
| ID: | 1490999525 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 163 (137) | ||
| Sequences: | 1084 (760.9) | ||
| Seq/Len: | 7.912 | ||
| Nf(neff/√len): | 65.0 |
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: 7.912).
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 |
| 15_L | 141_I | 2.573 | 1.00 |
| 94_L | 102_A | 2.508 | 1.00 |
| 107_L | 150_F | 2.435 | 1.00 |
| 123_I | 127_V | 2.283 | 1.00 |
| 88_Y | 138_T | 2.248 | 1.00 |
| 54_V | 128_L | 2.176 | 1.00 |
| 116_G | 120_L | 2.100 | 1.00 |
| 12_R | 145_L | 1.990 | 1.00 |
| 87_F | 113_S | 1.985 | 1.00 |
| 27_L | 82_I | 1.967 | 1.00 |
| 125_F | 131_F | 1.941 | 1.00 |
| 13_L | 92_L | 1.863 | 1.00 |
| 19_G | 141_I | 1.838 | 1.00 |
| 110_S | 145_L | 1.750 | 1.00 |
| 41_A | 134_V | 1.690 | 1.00 |
| 114_L | 118_V | 1.689 | 1.00 |
| 17_L | 21_V | 1.687 | 1.00 |
| 122_W | 127_V | 1.666 | 1.00 |
| 114_L | 146_M | 1.625 | 1.00 |
| 15_L | 145_L | 1.625 | 1.00 |
| 107_L | 111_L | 1.612 | 1.00 |
| 131_F | 136_I | 1.603 | 1.00 |
| 88_Y | 117_S | 1.574 | 1.00 |
| 44_D | 50_S | 1.547 | 1.00 |
| 18_T | 141_I | 1.528 | 1.00 |
| 30_K | 61_R | 1.524 | 1.00 |
| 54_V | 60_G | 1.458 | 0.99 |
| 43_C | 51_C | 1.406 | 0.99 |
| 121_A | 125_F | 1.404 | 0.99 |
| 15_L | 144_S | 1.403 | 0.99 |
| 27_L | 31_A | 1.394 | 0.99 |
| 110_S | 149_S | 1.389 | 0.99 |
| 91_Q | 145_L | 1.389 | 0.99 |
| 59_W | 123_I | 1.376 | 0.99 |
| 55_F | 81_S | 1.364 | 0.99 |
| 86_I | 90_L | 1.364 | 0.99 |
| 146_M | 150_F | 1.321 | 0.98 |
| 104_V | 108_L | 1.293 | 0.98 |
| 60_G | 128_L | 1.265 | 0.98 |
| 114_L | 143_V | 1.230 | 0.97 |
| 16_C | 91_Q | 1.220 | 0.97 |
| 136_I | 139_Y | 1.203 | 0.97 |
| 17_L | 92_L | 1.191 | 0.96 |
| 119_Y | 123_I | 1.169 | 0.96 |
| 19_G | 88_Y | 1.151 | 0.95 |
| 100_R | 104_V | 1.148 | 0.95 |
| 87_F | 109_S | 1.129 | 0.95 |
| 123_I | 128_L | 1.126 | 0.95 |
| 53_R | 130_D | 1.125 | 0.95 |
| 19_G | 138_T | 1.125 | 0.95 |
| 24_L | 28_H | 1.122 | 0.95 |
| 113_S | 142_N | 1.118 | 0.94 |
| 22_L | 137_T | 1.088 | 0.93 |
| 21_V | 32_A | 1.088 | 0.93 |
| 55_F | 124_L | 1.079 | 0.93 |
| 20_L | 85_C | 1.067 | 0.92 |
| 111_L | 146_M | 1.060 | 0.92 |
| 118_V | 122_W | 1.057 | 0.92 |
| 132_C | 135_C | 1.051 | 0.92 |
| 44_D | 52_S | 1.049 | 0.92 |
| 24_L | 82_I | 1.046 | 0.91 |
| 121_A | 124_L | 1.038 | 0.91 |
| 18_T | 94_L | 1.030 | 0.91 |
| 16_C | 95_G | 1.020 | 0.90 |
| 118_V | 121_A | 1.015 | 0.90 |
| 117_S | 143_V | 1.012 | 0.90 |
| 147_W | 151_R | 1.007 | 0.89 |
| 42_L | 134_V | 1.003 | 0.89 |
| 84_G | 139_Y | 1.000 | 0.89 |
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 | |
| 4nv5A | 2 | 0.816 | 99.9 | 0.396 | Contact Map |
| 2hi7B | 1 | 0.362 | 9.6 | 0.932 | Contact Map |
| 4ogqF | 1 | 0.1963 | 2.7 | 0.948 | Contact Map |
| 4n7bA | 1 | 0 | 2.3 | 0.95 | Contact Map |
| 4i0uA | 10 | 0.5828 | 1.4 | 0.956 | Contact Map |
| 3wu2L | 2 | 0.1718 | 1.1 | 0.959 | Contact Map |
| 4ev6A | 5 | 0.5951 | 1.1 | 0.959 | Contact Map |
| 1q90M | 1 | 0.2086 | 0.9 | 0.96 | Contact Map |
| 2rh1A | 1 | 0.9264 | 0.9 | 0.96 | Contact Map |
| 1wu0A | 1 | 0.1779 | 0.9 | 0.961 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)