| ns |
| ID: | 1457017043 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 39 (39) | ||
| Sequences: | 64 (52.8) | ||
| Seq/Len: | 1.641 | ||
| Nf(neff/√len): | 8.5 |
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: 1.641).
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 |
| 30_G | 35_G | 2.063 | 0.99 |
| 33_F | 39_F | 1.873 | 0.97 |
| 18_V | 21_S | 1.786 | 0.96 |
| 12_N | 30_G | 1.616 | 0.92 |
| 8_G | 24_S | 1.596 | 0.92 |
| 18_V | 27_Q | 1.588 | 0.91 |
| 6_G | 10_Q | 1.512 | 0.88 |
| 14_P | 21_S | 1.480 | 0.87 |
| 15_G | 20_K | 1.393 | 0.82 |
| 4_N | 10_Q | 1.390 | 0.82 |
| 30_G | 33_F | 1.358 | 0.80 |
| 34_S | 38_Y | 1.348 | 0.79 |
| 2_F | 10_Q | 1.272 | 0.73 |
| 13_A | 30_G | 1.243 | 0.71 |
| 11_L | 24_S | 1.218 | 0.69 |
| 11_L | 15_G | 1.176 | 0.65 |
| 17_T | 23_G | 1.142 | 0.61 |
| 19_N | 26_N | 1.128 | 0.60 |
| 4_N | 38_Y | 1.121 | 0.59 |
| 17_T | 32_N | 1.022 | 0.49 |
| 21_S | 31_A | 1.002 | 0.47 |
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 | |
| 4j94A | 1 | 1 | 1 | 0.898 | Contact Map |
| 3rlfF | 1 | 1 | 0.9 | 0.901 | Contact Map |
| 2wq4A | 3 | 0.1026 | 0.9 | 0.901 | Contact Map |
| 3fewX | 1 | 0 | 0.7 | 0.907 | Contact Map |
| 2e31A | 1 | 0.8718 | 0.7 | 0.907 | Contact Map |
| 2b6nA | 1 | 1 | 0.6 | 0.912 | Contact Map |
| 3kogA | 1 | 0.1282 | 0.6 | 0.912 | Contact Map |
| 4aybB | 1 | 0.8974 | 0.6 | 0.913 | Contact Map |
| 3p9yA | 4 | 0.6154 | 0.6 | 0.913 | Contact Map |
| 4qiwB | 2 | 0.8974 | 0.5 | 0.915 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)