| rdlB |
| ID: | 1510653865 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 50 (50) | ||
| Sequences: | 150 (63.2) | ||
| Seq/Len: | 3.000 | ||
| Nf(neff/√len): | 8.9 |
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: 3.000).
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 |
| 40_L | 46_G | 1.653 | 0.98 |
| 8_T | 23_S | 1.649 | 0.98 |
| 32_Q | 37_Q | 1.636 | 0.98 |
| 36_I | 40_L | 1.634 | 0.98 |
| 43_P | 46_G | 1.572 | 0.97 |
| 5_R | 47_L | 1.549 | 0.97 |
| 15_G | 35_L | 1.546 | 0.97 |
| 3_G | 6_H | 1.502 | 0.96 |
| 8_T | 48_P | 1.474 | 0.95 |
| 20_F | 23_S | 1.407 | 0.93 |
| 28_Y | 34_G | 1.387 | 0.93 |
| 16_A | 32_Q | 1.359 | 0.92 |
| 8_T | 50_K | 1.325 | 0.90 |
| 33_I | 40_L | 1.243 | 0.86 |
| 34_G | 39_S | 1.242 | 0.86 |
| 22_N | 35_L | 1.238 | 0.86 |
| 14_N | 37_Q | 1.211 | 0.84 |
| 7_G | 23_S | 1.146 | 0.79 |
| 6_H | 10_T | 1.140 | 0.79 |
| 2_A | 5_R | 1.114 | 0.76 |
| 28_Y | 40_L | 1.108 | 0.76 |
| 28_Y | 35_L | 1.095 | 0.75 |
| 35_L | 43_P | 1.092 | 0.74 |
| 8_T | 49_A | 1.067 | 0.72 |
| 36_I | 43_P | 1.058 | 0.71 |
| 33_I | 38_G | 1.056 | 0.71 |
| 31_P | 42_K | 1.053 | 0.70 |
| 12_N | 46_G | 1.028 | 0.68 |
| 38_G | 43_P | 1.021 | 0.67 |
| 2_A | 10_T | 1.021 | 0.67 |
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 | |
| 3d3rA | 2 | 0.3 | 3.8 | 0.913 | Contact Map |
| 2x24A | 2 | 0.8 | 1.9 | 0.925 | Contact Map |
| 1spvA | 1 | 0.36 | 1.9 | 0.926 | Contact Map |
| 1zxxA | 1 | 0.54 | 1.7 | 0.927 | Contact Map |
| 4i7eA | 4 | 0.54 | 1.6 | 0.928 | Contact Map |
| 2p2vA | 1 | 0.42 | 1.6 | 0.929 | Contact Map |
| 1pfkA | 2 | 0.54 | 1.6 | 0.929 | Contact Map |
| 4xz2A | 4 | 0 | 1.5 | 0.93 | Contact Map |
| 2a1vA | 1 | 0.32 | 1.4 | 0.932 | Contact Map |
| 2higA | 2 | 0.66 | 1.3 | 0.932 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)