| 1_1ayipdb |
| ID: | 1516869498 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 86 (82) | ||
| Sequences: | 311 (249.8) | ||
| Seq/Len: | 3.793 | ||
| Nf(neff/√len): | 27.6 |
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: 3.793).
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 | 3.179 | 1.00 |
| 70_K | 74_E | 3.057 | 1.00 |
| 46_E | 81_K | 2.630 | 1.00 |
| 40_H | 44_I | 2.305 | 1.00 |
| 74_E | 78_A | 2.273 | 1.00 |
| 64_S | 67_G | 2.149 | 1.00 |
| 78_A | 83_G | 1.856 | 1.00 |
| 12_E | 73_K | 1.811 | 0.99 |
| 61_R | 71_E | 1.743 | 0.99 |
| 78_A | 86_Q | 1.722 | 0.99 |
| 79_N | 83_G | 1.675 | 0.99 |
| 40_H | 43_K | 1.662 | 0.99 |
| 42_V | 51_T | 1.613 | 0.98 |
| 70_K | 78_A | 1.607 | 0.98 |
| 20_K | 65_P | 1.584 | 0.98 |
| 17_Q | 20_K | 1.555 | 0.98 |
| 20_K | 66_E | 1.554 | 0.98 |
| 49_D | 58_S | 1.542 | 0.98 |
| 63_D | 67_G | 1.508 | 0.97 |
| 60_N | 64_S | 1.360 | 0.94 |
| 21_E | 33_V | 1.313 | 0.93 |
| 52_D | 56_Y | 1.258 | 0.91 |
| 41_F | 50_G | 1.257 | 0.91 |
| 41_F | 47_H | 1.253 | 0.91 |
| 23_E | 62_D | 1.239 | 0.90 |
| 57_P | 63_D | 1.163 | 0.86 |
| 68_I | 71_E | 1.154 | 0.85 |
| 28_A | 86_Q | 1.152 | 0.85 |
| 15_F | 41_F | 1.139 | 0.84 |
| 21_E | 37_L | 1.101 | 0.81 |
| 37_L | 40_H | 1.087 | 0.80 |
| 17_Q | 68_I | 1.083 | 0.80 |
| 50_G | 53_L | 1.076 | 0.79 |
| 77_A | 83_G | 1.068 | 0.78 |
| 15_F | 44_I | 1.060 | 0.78 |
| 35_D | 39_E | 1.049 | 0.77 |
| 35_D | 38_L | 1.040 | 0.76 |
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 | 0.9651 | 100 | 0.023 | Contact Map |
| 1unkA | 4 | 0.9884 | 100 | 0.026 | Contact Map |
| 1gxgA | 1 | 0.9767 | 100 | 0.03 | Contact Map |
| 4f37A | 2 | 1 | 100 | 0.035 | Contact Map |
| 3u43A | 1 | 0.9651 | 100 | 0.037 | Contact Map |
| 4uhpB | 4 | 0 | 100 | 0.04 | Contact Map |
| 4qkoA | 4 | 0 | 100 | 0.065 | Contact Map |
| 2k0dX | 1 | 0.9884 | 100 | 0.065 | Contact Map |
| 4h3kB | 2 | 0.6279 | 31.7 | 0.9 | Contact Map |
| 3p9yA | 4 | 0.6279 | 22.3 | 0.907 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)