| DIP13 |
| ID: | 1518692509 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 86 (84) | ||
| Sequences: | 125 (89.2) | ||
| Seq/Len: | 1.488 | ||
| Nf(neff/√len): | 9.7 |
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: 1.488).
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 |
| 70_I | 73_S | 2.167 | 0.99 |
| 17_Q | 29_T | 1.742 | 0.94 |
| 76_T | 84_E | 1.586 | 0.90 |
| 31_E | 34_I | 1.569 | 0.89 |
| 14_I | 56_Y | 1.526 | 0.87 |
| 73_S | 81_L | 1.513 | 0.87 |
| 28_I | 42_V | 1.508 | 0.86 |
| 56_Y | 67_Y | 1.420 | 0.82 |
| 11_R | 57_D | 1.416 | 0.81 |
| 80_V | 84_E | 1.389 | 0.80 |
| 7_L | 67_Y | 1.383 | 0.79 |
| 38_R | 60_I | 1.362 | 0.78 |
| 47_A | 63_T | 1.350 | 0.77 |
| 10_K | 38_R | 1.326 | 0.75 |
| 27_K | 35_L | 1.307 | 0.73 |
| 10_K | 60_I | 1.289 | 0.72 |
| 18_L | 53_K | 1.271 | 0.71 |
| 22_D | 58_K | 1.266 | 0.70 |
| 45_S | 57_D | 1.251 | 0.69 |
| 71_L | 82_K | 1.248 | 0.68 |
| 8_R | 33_Q | 1.244 | 0.68 |
| 33_Q | 40_A | 1.240 | 0.68 |
| 37_K | 41_Q | 1.183 | 0.62 |
| 70_I | 84_E | 1.175 | 0.62 |
| 76_T | 80_V | 1.158 | 0.60 |
| 7_L | 11_R | 1.154 | 0.60 |
| 22_D | 53_K | 1.101 | 0.54 |
| 73_S | 77_L | 1.101 | 0.54 |
| 32_L | 41_Q | 1.077 | 0.52 |
| 28_I | 52_T | 1.072 | 0.51 |
| 21_D | 45_S | 1.071 | 0.51 |
| 10_K | 57_D | 1.069 | 0.51 |
| 70_I | 78_L | 1.061 | 0.50 |
| 49_K | 62_E | 1.059 | 0.50 |
| 32_L | 49_K | 1.054 | 0.49 |
| 77_L | 82_K | 1.049 | 0.49 |
| 27_K | 50_T | 1.046 | 0.49 |
| 8_R | 20_E | 1.040 | 0.48 |
| 60_I | 72_E | 1.035 | 0.47 |
| 56_Y | 79_T | 1.035 | 0.47 |
| 30_Q | 33_Q | 1.024 | 0.46 |
| 14_I | 86_V | 1.017 | 0.46 |
| 8_R | 61_S | 1.015 | 0.45 |
| 48_R | 58_K | 1.014 | 0.45 |
| 76_T | 81_L | 1.013 | 0.45 |
| 7_L | 35_L | 1.006 | 0.44 |
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 | |
| 4rh7A | 1 | 0.9535 | 78.8 | 0.853 | Contact Map |
| 3ghgA | 4 | 0.686 | 74.2 | 0.858 | Contact Map |
| 4cgkA | 2 | 0.7907 | 55.6 | 0.874 | Contact Map |
| 1deqA | 4 | 1 | 54.9 | 0.875 | Contact Map |
| 4q4gX | 1 | 0 | 51.9 | 0.877 | Contact Map |
| 1i84S | 2 | 0 | 50.1 | 0.878 | Contact Map |
| 3ojaB | 1 | 0.9535 | 49.1 | 0.879 | Contact Map |
| 2dfsA | 2 | 0.907 | 47.4 | 0.88 | Contact Map |
| 3vkgA | 2 | 0.9535 | 41.5 | 0.884 | Contact Map |
| 3ojaA | 1 | 0.9535 | 29.9 | 0.893 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)