| pcsk9 pro domain10 |
| ID: | 1456399456 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 122 (83) | ||
| Sequences: | 4158 (2490.6) | ||
| Seq/Len: | 50.096 | ||
| Nf(neff/√len): | 273.4 |
HHblits Results: (2015_06)
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: 50.096).
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 |
| 51_V | 112_Y | 4.206 | 1.00 |
| 47_T | 116_D | 2.929 | 1.00 |
| 97_S | 100_L | 2.842 | 1.00 |
| 53_K | 111_D | 2.631 | 1.00 |
| 110_V | 113_I | 2.592 | 1.00 |
| 43_R | 115_E | 2.503 | 1.00 |
| 46_G | 115_E | 2.361 | 1.00 |
| 85_F | 93_L | 2.353 | 1.00 |
| 101_L | 105_L | 2.314 | 1.00 |
| 51_V | 111_D | 2.197 | 1.00 |
| 47_T | 95_K | 2.039 | 1.00 |
| 47_T | 82_L | 2.000 | 1.00 |
| 102_E | 105_L | 1.977 | 1.00 |
| 101_L | 104_A | 1.912 | 1.00 |
| 116_D | 119_V | 1.904 | 1.00 |
| 101_L | 113_I | 1.860 | 1.00 |
| 64_T | 92_F | 1.834 | 1.00 |
| 46_G | 98_G | 1.561 | 1.00 |
| 52_L | 92_F | 1.538 | 1.00 |
| 83_H | 93_L | 1.488 | 1.00 |
| 96_M | 101_L | 1.454 | 1.00 |
| 102_E | 106_K | 1.367 | 0.99 |
| 53_K | 109_H | 1.353 | 0.99 |
| 81_I | 84_V | 1.304 | 0.99 |
| 82_L | 95_K | 1.302 | 0.99 |
| 82_L | 93_L | 1.289 | 0.99 |
| 47_T | 93_L | 1.263 | 0.99 |
| 103_L | 106_K | 1.236 | 0.98 |
| 57_H | 60_Q | 1.220 | 0.98 |
| 52_L | 61_S | 1.204 | 0.98 |
| 39_K | 42_W | 1.202 | 0.98 |
| 51_V | 89_L | 1.187 | 0.98 |
| 64_T | 67_R | 1.181 | 0.98 |
| 44_L | 47_T | 1.135 | 0.97 |
| 101_L | 110_V | 1.097 | 0.96 |
| 85_F | 91_G | 1.053 | 0.95 |
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 | |
| 4nmxA | 1 | 0.7541 | 99.8 | 0.291 | Contact Map |
| 2p4eP | 2 | 0.7541 | 99.5 | 0.438 | Contact Map |
| 2w2nP | 1 | 0.7623 | 99.5 | 0.443 | Contact Map |
| 1v5iB | 1 | 0.5984 | 99 | 0.572 | Contact Map |
| 3cnqP | 1 | 0.5656 | 98.8 | 0.595 | Contact Map |
| 2z30B | 1 | 0.5328 | 98.7 | 0.616 | Contact Map |
| 3whiA | 2 | 0.5902 | 98.4 | 0.648 | Contact Map |
| 3wiuA | 3 | 0.541 | 97.9 | 0.693 | Contact Map |
| 3afgA | 2 | 0.7705 | 97.6 | 0.711 | Contact Map |
| 1r6vA | 1 | 0.7787 | 95.7 | 0.771 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)