| IS-inefficient |
| ID: | 1488088069 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 40 (40) | ||
| Sequences: | 675 (675) | ||
| Seq/Len: | 16.875 | ||
| Nf(neff/√len): | 106.7 |
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: 16.875).
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 |
| 6_G | 21_G | 2.029 | 1.00 |
| 31_G | 34_T | 1.913 | 1.00 |
| 3_A | 20_A | 1.829 | 1.00 |
| 14_G | 23_G | 1.674 | 1.00 |
| 1_C | 17_A | 1.541 | 1.00 |
| 22_C | 31_G | 1.510 | 1.00 |
| 9_A | 16_C | 1.490 | 1.00 |
| 5_G | 19_A | 1.436 | 1.00 |
| 34_T | 37_G | 1.348 | 0.99 |
| 4_G | 7_A | 1.243 | 0.98 |
| 27_C | 30_T | 1.228 | 0.98 |
| 1_C | 20_A | 1.171 | 0.98 |
| 2_C | 11_C | 1.122 | 0.97 |
| 3_A | 21_G | 1.121 | 0.97 |
| 3_A | 16_C | 1.095 | 0.96 |
| 8_C | 40_T | 1.087 | 0.96 |
| 2_C | 31_G | 1.085 | 0.96 |
| 12_T | 15_G | 1.067 | 0.95 |
| 26_A | 34_T | 1.026 | 0.94 |
| 11_C | 40_T | 1.012 | 0.93 |
| 11_C | 35_A | 1.006 | 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 | |
| 4kblA | 2 | 0 | 0.2 | 0.663 | Contact Map |
| 2pk2A | 4 | 0 | 0.2 | 0.669 | Contact Map |
| 1cn3F | 1 | 0.25 | 0.1 | 0.712 | Contact Map |
| 1t2yA | 1 | 0.4 | 0.1 | 0.766 | Contact Map |
| 1airA | 1 | 0.6 | 0.1 | 0.772 | Contact Map |
| 4ma7A | 1 | 0.325 | 0.1 | 0.794 | Contact Map |
| 1s58A | 1 | 0.125 | 0.1 | 0.815 | Contact Map |
| 2wolA | 1 | 0.425 | 0.1 | 0.815 | Contact Map |
| 1x0gA | 4 | 0.4 | 0.1 | 0.821 | Contact Map |
| 2qy1A | 2 | 0.475 | 0.1 | 0.842 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)