| pqqd |
| ID: | 1485553039 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 92 (88) | ||
| Sequences: | 1015 (791.9) | ||
| Seq/Len: | 11.534 | ||
| Nf(neff/√len): | 84.4 |
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: 11.534).
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 |
| 57_A | 67_G | 2.689 | 1.00 |
| 51_D | 54_A | 2.298 | 1.00 |
| 50_R | 58_M | 2.015 | 1.00 |
| 65_E | 69_V | 1.927 | 1.00 |
| 45_L | 58_M | 1.852 | 1.00 |
| 17_W | 22_E | 1.809 | 1.00 |
| 41_A | 45_L | 1.800 | 1.00 |
| 45_L | 62_R | 1.775 | 1.00 |
| 67_G | 70_D | 1.762 | 1.00 |
| 70_D | 74_V | 1.687 | 1.00 |
| 9_F | 43_L | 1.683 | 1.00 |
| 56_I | 70_D | 1.618 | 1.00 |
| 52_V | 74_V | 1.583 | 1.00 |
| 41_A | 44_E | 1.527 | 1.00 |
| 56_I | 73_V | 1.519 | 1.00 |
| 19_A | 22_E | 1.478 | 1.00 |
| 46_V | 55_I | 1.446 | 1.00 |
| 41_A | 62_R | 1.414 | 1.00 |
| 78_Q | 82_Q | 1.407 | 0.99 |
| 2_Q | 5_S | 1.387 | 0.99 |
| 53_A | 70_D | 1.369 | 0.99 |
| 74_V | 78_Q | 1.302 | 0.99 |
| 42_I | 76_F | 1.265 | 0.99 |
| 50_R | 54_A | 1.265 | 0.99 |
| 39_A | 76_F | 1.264 | 0.99 |
| 79_I | 82_Q | 1.261 | 0.99 |
| 52_V | 77_L | 1.220 | 0.98 |
| 59_L | 73_V | 1.197 | 0.98 |
| 24_H | 40_A | 1.182 | 0.98 |
| 15_L | 43_L | 1.174 | 0.98 |
| 78_Q | 81_C | 1.174 | 0.98 |
| 8_A | 87_T | 1.160 | 0.97 |
| 7_V | 88_C | 1.145 | 0.97 |
| 13_Y | 26_I | 1.115 | 0.96 |
| 16_Q | 32_M | 1.109 | 0.96 |
| 60_N | 69_V | 1.080 | 0.95 |
| 2_Q | 6_I | 1.061 | 0.95 |
| 21_Q | 28_Y | 1.060 | 0.95 |
| 69_V | 72_D | 1.048 | 0.94 |
| 42_I | 83_Q | 1.016 | 0.93 |
| 45_L | 55_I | 1.003 | 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 | |
| 3g2bA | 1 | 0.9565 | 99.8 | 0.165 | Contact Map |
| 4v1tA | 2 | 0.8913 | 96.7 | 0.698 | Contact Map |
| 3h5nA | 4 | 0.8478 | 93.9 | 0.751 | Contact Map |
| 4wd9A | 2 | 0.9348 | 90.3 | 0.776 | Contact Map |
| 3deeA | 1 | 0.9891 | 86.5 | 0.79 | Contact Map |
| 4cswA | 2 | 0.8913 | 78.5 | 0.809 | Contact Map |
| 2g9wA | 2 | 0.6196 | 61.7 | 0.831 | Contact Map |
| 1p6rA | 1 | 0.663 | 56.5 | 0.836 | Contact Map |
| 2mh2A | 1 | 0.5761 | 53 | 0.84 | Contact Map |
| 2co5A | 2 | 0.6848 | 51.7 | 0.841 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)