| RWD |
| ID: | 1512490500 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 50 (50) | ||
| Sequences: | 251 (237) | ||
| Seq/Len: | 5.020 | ||
| Nf(neff/√len): | 33.5 |
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: 5.020).
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 |
| 3_R | 8_R | 2.377 | 1.00 |
| 17_L | 25_T | 1.835 | 1.00 |
| 2_Y | 38_F | 1.637 | 0.99 |
| 6_G | 47_R | 1.636 | 0.99 |
| 39_F | 43_Y | 1.569 | 0.99 |
| 13_N | 38_F | 1.508 | 0.99 |
| 29_L | 48_I | 1.470 | 0.98 |
| 8_R | 22_E | 1.379 | 0.97 |
| 7_V | 36_T | 1.373 | 0.97 |
| 30_P | 42_K | 1.357 | 0.97 |
| 10_D | 14_N | 1.334 | 0.96 |
| 23_L | 29_L | 1.333 | 0.96 |
| 7_V | 45_W | 1.310 | 0.96 |
| 43_Y | 47_R | 1.262 | 0.94 |
| 11_L | 43_Y | 1.187 | 0.92 |
| 15_Q | 50_K | 1.182 | 0.92 |
| 32_E | 37_E | 1.118 | 0.88 |
| 7_V | 10_D | 1.106 | 0.87 |
| 18_I | 43_Y | 1.066 | 0.85 |
| 9_L | 29_L | 1.064 | 0.85 |
| 5_L | 28_T | 1.052 | 0.84 |
| 10_D | 43_Y | 1.047 | 0.83 |
| 9_L | 25_T | 1.047 | 0.83 |
| 45_W | 49_G | 1.029 | 0.82 |
| 19_Q | 24_G | 1.025 | 0.81 |
| 46_S | 49_G | 1.022 | 0.81 |
| 17_L | 23_L | 1.016 | 0.81 |
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 | |
| 4geqB | 2 | 0.98 | 92.8 | 0.334 | Contact Map |
| 2fv4B | 1 | 1 | 92.6 | 0.339 | Contact Map |
| 2ftxB | 1 | 1 | 92.4 | 0.343 | Contact Map |
| 3vz9D | 1 | 1 | 71.1 | 0.499 | Contact Map |
| 3vz9B | 1 | 0.98 | 51.1 | 0.558 | Contact Map |
| 2ve7C | 2 | 0.98 | 49.8 | 0.561 | Contact Map |
| 2ve7A | 2 | 0.98 | 39.6 | 0.588 | Contact Map |
| 4dzoA | 2 | 0.96 | 37.1 | 0.594 | Contact Map |
| 1nktA | 2 | 0.88 | 8.8 | 0.697 | Contact Map |
| 1o22A | 1 | 0.78 | 4.1 | 0.74 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)