| 5j8y |
| ID: | 1475697827 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 80 (74) | ||
| Sequences: | 477 (312) | ||
| Seq/Len: | 6.446 | ||
| Nf(neff/√len): | 36.3 |
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: 6.446).
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 |
| 12_E | 33_R | 2.207 | 1.00 |
| 15_I | 29_G | 1.907 | 1.00 |
| 59_G | 63_K | 1.731 | 1.00 |
| 22_D | 25_L | 1.600 | 1.00 |
| 35_H | 42_L | 1.527 | 0.99 |
| 9_W | 14_V | 1.507 | 0.99 |
| 3_D | 30_D | 1.450 | 0.99 |
| 49_M | 65_C | 1.417 | 0.99 |
| 39_G | 45_L | 1.379 | 0.98 |
| 68_V | 71_V | 1.370 | 0.98 |
| 48_E | 51_M | 1.366 | 0.98 |
| 37_I | 54_M | 1.333 | 0.98 |
| 21_N | 24_S | 1.320 | 0.98 |
| 6_P | 68_V | 1.317 | 0.98 |
| 14_V | 17_Y | 1.310 | 0.97 |
| 47_S | 50_M | 1.290 | 0.97 |
| 60_P | 63_K | 1.243 | 0.96 |
| 65_C | 69_N | 1.236 | 0.96 |
| 18_I | 22_D | 1.211 | 0.95 |
| 19_E | 46_N | 1.206 | 0.95 |
| 10_T | 73_G | 1.204 | 0.95 |
| 42_L | 66_N | 1.187 | 0.95 |
| 51_M | 65_C | 1.159 | 0.94 |
| 36_E | 41_A | 1.152 | 0.93 |
| 50_M | 72_N | 1.138 | 0.93 |
| 43_L | 63_K | 1.138 | 0.93 |
| 70_K | 75_R | 1.129 | 0.93 |
| 39_G | 59_G | 1.117 | 0.92 |
| 11_I | 14_V | 1.088 | 0.91 |
| 6_P | 9_W | 1.072 | 0.90 |
| 54_M | 63_K | 1.064 | 0.89 |
| 54_M | 61_A | 1.057 | 0.89 |
| 16_Q | 19_E | 1.049 | 0.88 |
| 41_A | 44_L | 1.047 | 0.88 |
| 31_L | 56_L | 1.030 | 0.87 |
| 38_D | 58_E | 1.022 | 0.87 |
| 37_I | 63_K | 1.013 | 0.86 |
| 25_L | 28_H | 1.004 | 0.85 |
| 60_P | 64_I | 1.001 | 0.85 |
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 | |
| 1pk1B | 2 | 0.875 | 99.7 | 0.329 | Contact Map |
| 4pzoA | 6 | 0.9 | 99.7 | 0.345 | Contact Map |
| 1kw4A | 1 | 0.875 | 99.6 | 0.393 | Contact Map |
| 2dkzA | 1 | 0.925 | 99.5 | 0.399 | Contact Map |
| 3bs5A | 1 | 0.9625 | 99.3 | 0.464 | Contact Map |
| 4z8lC | 2 | 0 | 99.3 | 0.476 | Contact Map |
| 2e8oA | 1 | 0.9625 | 99.3 | 0.477 | Contact Map |
| 2eanA | 1 | 0.9875 | 99.3 | 0.48 | Contact Map |
| 3bs7A | 2 | 0.925 | 99.3 | 0.484 | Contact Map |
| 2d8cA | 1 | 0.95 | 99.3 | 0.486 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)