| demharters3_cox6a2 |
| ID: | 1496645913 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 94 (82) | ||
| Sequences: | 397 (225.7) | ||
| Seq/Len: | 4.841 | ||
| Nf(neff/√len): | 24.9 |
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: 4.841).
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 |
| 23_N | 27_L | 1.946 | 1.00 |
| 25_W | 29_T | 1.873 | 1.00 |
| 73_D | 76_H | 1.800 | 1.00 |
| 27_L | 31_V | 1.785 | 1.00 |
| 16_D | 20_A | 1.703 | 0.99 |
| 80_H | 87_L | 1.626 | 0.99 |
| 77_T | 81_N | 1.625 | 0.99 |
| 56_F | 86_P | 1.585 | 0.99 |
| 26_R | 31_V | 1.556 | 0.99 |
| 62_L | 75_N | 1.551 | 0.99 |
| 65_R | 75_N | 1.489 | 0.98 |
| 50_H | 53_R | 1.469 | 0.98 |
| 29_T | 34_L | 1.446 | 0.98 |
| 45_W | 49_G | 1.337 | 0.96 |
| 80_H | 88_P | 1.327 | 0.96 |
| 79_F | 85_N | 1.305 | 0.95 |
| 24_T | 31_V | 1.289 | 0.95 |
| 15_G | 18_G | 1.276 | 0.94 |
| 76_H | 80_H | 1.275 | 0.94 |
| 29_T | 33_A | 1.262 | 0.94 |
| 36_S | 60_H | 1.233 | 0.93 |
| 44_C | 48_A | 1.216 | 0.92 |
| 77_T | 80_H | 1.179 | 0.91 |
| 23_N | 31_V | 1.161 | 0.90 |
| 41_S | 47_H | 1.150 | 0.89 |
| 33_A | 36_S | 1.148 | 0.89 |
| 81_N | 85_N | 1.137 | 0.89 |
| 26_R | 37_V | 1.112 | 0.87 |
| 74_G | 81_N | 1.097 | 0.86 |
| 63_R | 86_P | 1.090 | 0.86 |
| 36_S | 39_L | 1.087 | 0.86 |
| 33_A | 73_D | 1.075 | 0.85 |
| 86_P | 90_G | 1.074 | 0.85 |
| 58_P | 62_L | 1.073 | 0.84 |
| 88_P | 92_E | 1.053 | 0.83 |
| 86_P | 89_T | 1.050 | 0.83 |
| 79_F | 82_P | 1.041 | 0.82 |
| 13_S | 16_D | 1.035 | 0.81 |
| 80_H | 85_N | 1.030 | 0.81 |
| 54_P | 91_Y | 1.025 | 0.81 |
| 79_F | 84_V | 1.023 | 0.80 |
| 36_S | 58_P | 1.022 | 0.80 |
| 43_N | 46_M | 1.021 | 0.80 |
| 74_G | 80_H | 1.006 | 0.79 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2y69G | 2 | 0.883 | 100 | 0.051 | Contact Map |
| 1v54G | 2 | 0.883 | 100 | 0.109 | Contact Map |
| 2kv9B | 1 | 0.5745 | 15.9 | 0.926 | Contact Map |
| 1s4xA | 1 | 0.5 | 12.8 | 0.929 | Contact Map |
| 2a2mA | 2 | 0.3298 | 11.4 | 0.931 | Contact Map |
| 4xtrG | 1 | 0.234 | 5.8 | 0.94 | Contact Map |
| 4fmvA | 1 | 0.4894 | 4.2 | 0.944 | Contact Map |
| 2kncB | 1 | 0.8085 | 3.9 | 0.945 | Contact Map |
| 1xq4A | 4 | 0.3936 | 3.4 | 0.946 | Contact Map |
| 4tnwA | 10 | 0.4574 | 3.4 | 0.946 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)