| ily |
| ID: | 1490003131 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 42 (40) | ||
| Sequences: | 61 (54.7) | ||
| Seq/Len: | 1.525 | ||
| Nf(neff/√len): | 8.6 |
Jackhmmer Results: (2016_04)
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: 1.525).
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 |
| 21_Q | 30_Q | 2.620 | 1.00 |
| 18_G | 23_I | 2.041 | 0.98 |
| 25_K | 41_Q | 1.658 | 0.93 |
| 5_F | 36_F | 1.608 | 0.91 |
| 21_Q | 24_S | 1.600 | 0.91 |
| 7_S | 36_F | 1.558 | 0.89 |
| 29_N | 33_G | 1.469 | 0.85 |
| 3_S | 32_P | 1.431 | 0.83 |
| 12_D | 29_N | 1.404 | 0.81 |
| 8_Y | 30_Q | 1.316 | 0.75 |
| 17_P | 32_P | 1.274 | 0.71 |
| 5_F | 13_Q | 1.251 | 0.69 |
| 13_Q | 18_G | 1.216 | 0.66 |
| 11_G | 27_S | 1.203 | 0.65 |
| 24_S | 35_T | 1.188 | 0.64 |
| 11_G | 18_G | 1.182 | 0.63 |
| 4_S | 7_S | 1.162 | 0.61 |
| 14_F | 21_Q | 1.149 | 0.60 |
| 17_P | 24_S | 1.133 | 0.58 |
| 31_F | 36_F | 1.108 | 0.56 |
| 33_G | 38_G | 1.084 | 0.53 |
| 22_N | 29_N | 1.055 | 0.50 |
| 36_F | 40_V | 1.023 | 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 | |
| 4uypA | 2 | 0.5476 | 1.6 | 0.902 | Contact Map |
| 3kogA | 1 | 0.1905 | 1.3 | 0.907 | Contact Map |
| 3cslA | 2 | 0.8571 | 1.2 | 0.908 | Contact Map |
| 3kcpA | 1 | 0.5476 | 1 | 0.912 | Contact Map |
| 3v8xA | 1 | 0.8571 | 1 | 0.912 | Contact Map |
| 1fzdA | 8 | 0.381 | 1 | 0.913 | Contact Map |
| 2cclA | 2 | 0.5476 | 0.9 | 0.916 | Contact Map |
| 2wq4A | 3 | 0.0952 | 0.9 | 0.916 | Contact Map |
| 4j94A | 1 | 1 | 0.9 | 0.917 | Contact Map |
| 2h9xA | 1 | 0.5476 | 0.8 | 0.917 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)