| 1AYI |
| ID: | 1471608275 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 87 (82) | ||
| Sequences: | 301 (246.5) | ||
| Seq/Len: | 3.671 | ||
| Nf(neff/√len): | 27.2 |
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: 3.671).
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 |
| 19_L | 69_V | 3.244 | 1.00 |
| 70_K | 74_E | 2.815 | 1.00 |
| 46_E | 81_K | 2.479 | 1.00 |
| 40_H | 44_I | 2.275 | 1.00 |
| 74_E | 78_A | 2.252 | 1.00 |
| 64_S | 67_G | 2.162 | 1.00 |
| 40_H | 43_K | 1.796 | 0.99 |
| 61_R | 71_E | 1.729 | 0.99 |
| 78_A | 86_Q | 1.675 | 0.99 |
| 49_D | 58_S | 1.664 | 0.99 |
| 42_V | 51_T | 1.626 | 0.98 |
| 79_N | 83_G | 1.589 | 0.98 |
| 20_K | 66_E | 1.574 | 0.98 |
| 78_A | 83_G | 1.562 | 0.98 |
| 12_E | 73_K | 1.561 | 0.98 |
| 17_Q | 20_K | 1.540 | 0.98 |
| 63_D | 67_G | 1.448 | 0.96 |
| 70_K | 78_A | 1.402 | 0.95 |
| 21_E | 33_V | 1.362 | 0.94 |
| 15_F | 41_F | 1.346 | 0.94 |
| 20_K | 65_P | 1.283 | 0.91 |
| 23_E | 62_D | 1.268 | 0.91 |
| 50_G | 53_L | 1.188 | 0.87 |
| 78_A | 87_G | 1.186 | 0.86 |
| 46_E | 76_R | 1.159 | 0.85 |
| 52_D | 56_Y | 1.144 | 0.84 |
| 37_L | 40_H | 1.141 | 0.83 |
| 28_A | 86_Q | 1.123 | 0.82 |
| 22_I | 30_T | 1.119 | 0.82 |
| 41_F | 47_H | 1.101 | 0.80 |
| 17_Q | 68_I | 1.100 | 0.80 |
| 77_A | 83_G | 1.085 | 0.79 |
| 57_P | 63_D | 1.079 | 0.78 |
| 41_F | 50_G | 1.039 | 0.75 |
| 35_D | 39_E | 1.035 | 0.74 |
| 23_E | 68_I | 1.031 | 0.74 |
| 18_L | 41_F | 1.029 | 0.74 |
| 60_N | 64_S | 1.027 | 0.74 |
| 38_L | 55_Y | 1.003 | 0.71 |
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 | |
| 1fr2A | 1 | 0.954 | 100 | 0.018 | Contact Map |
| 1unkA | 4 | 0.9885 | 100 | 0.022 | Contact Map |
| 1gxgA | 1 | 0.977 | 100 | 0.028 | Contact Map |
| 4f37A | 2 | 0.9885 | 100 | 0.028 | Contact Map |
| 3u43A | 1 | 0.9655 | 100 | 0.03 | Contact Map |
| 4uhpB | 4 | 0 | 100 | 0.032 | Contact Map |
| 4qkoA | 4 | 0 | 100 | 0.056 | Contact Map |
| 2k0dX | 1 | 0.9885 | 100 | 0.072 | Contact Map |
| 5ajtA | 4 | 0 | 22.9 | 0.906 | Contact Map |
| 4h3kB | 2 | 0.6207 | 20.7 | 0.908 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)