| Gas Protein |
| ID: | 1424433035 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 75 (70) | ||
| Sequences: | 149 (61.8) | ||
| Seq/Len: | 2.129 | ||
| Nf(neff/√len): | 7.4 |
Jackhmmer Results: (2015_01_07)
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: 2.129).
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 |
| 28_V | 36_L | 1.917 | 0.99 |
| 51_L | 54_A | 1.795 | 0.98 |
| 38_V | 44_A | 1.678 | 0.96 |
| 39_E | 53_Y | 1.653 | 0.96 |
| 4_D | 10_E | 1.582 | 0.94 |
| 28_V | 35_I | 1.516 | 0.92 |
| 25_W | 39_E | 1.418 | 0.89 |
| 58_A | 61_E | 1.413 | 0.89 |
| 12_L | 15_V | 1.396 | 0.88 |
| 18_K | 37_T | 1.391 | 0.87 |
| 28_V | 34_E | 1.372 | 0.86 |
| 14_R | 53_Y | 1.324 | 0.84 |
| 12_L | 17_D | 1.309 | 0.83 |
| 31_V | 51_L | 1.290 | 0.82 |
| 37_T | 48_D | 1.279 | 0.81 |
| 52_H | 56_E | 1.275 | 0.80 |
| 15_V | 41_R | 1.275 | 0.80 |
| 13_D | 18_K | 1.259 | 0.79 |
| 15_V | 54_A | 1.250 | 0.79 |
| 53_Y | 58_A | 1.227 | 0.77 |
| 18_K | 35_I | 1.216 | 0.76 |
| 25_W | 57_I | 1.204 | 0.75 |
| 7_G | 59_K | 1.203 | 0.75 |
| 39_E | 59_K | 1.189 | 0.74 |
| 32_G | 49_T | 1.154 | 0.70 |
| 32_G | 45_A | 1.136 | 0.69 |
| 14_R | 39_E | 1.120 | 0.67 |
| 9_A | 18_K | 1.100 | 0.65 |
| 10_E | 39_E | 1.089 | 0.64 |
| 26_A | 30_L | 1.073 | 0.62 |
| 47_V | 55_E | 1.072 | 0.62 |
| 31_V | 54_A | 1.069 | 0.62 |
| 35_I | 48_D | 1.068 | 0.62 |
| 34_E | 43_V | 1.066 | 0.61 |
| 5_S | 26_A | 1.047 | 0.59 |
| 68_G | 71_A | 1.042 | 0.59 |
| 20_V | 47_V | 1.009 | 0.55 |
| 56_E | 59_K | 1.009 | 0.55 |
| 41_R | 54_A | 1.006 | 0.55 |
| 30_L | 37_T | 1.004 | 0.55 |
| 11_V | 51_L | 1.002 | 0.54 |
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 | |
| 1vjoA | 1 | 0.6933 | 13.5 | 0.908 | Contact Map |
| 2aeuA | 1 | 0.76 | 11.6 | 0.911 | Contact Map |
| 2qmxA | 2 | 0.8267 | 8 | 0.917 | Contact Map |
| 3e9kA | 1 | 0.7067 | 7.9 | 0.917 | Contact Map |
| 3cq5A | 3 | 0.68 | 7.5 | 0.918 | Contact Map |
| 4bm1A | 2 | 0.9067 | 6.2 | 0.921 | Contact Map |
| 4m2mA | 1 | 0.72 | 6.2 | 0.921 | Contact Map |
| 3q3uA | 1 | 0.9067 | 5.8 | 0.922 | Contact Map |
| 2yrrA | 2 | 0.6933 | 5.7 | 0.922 | Contact Map |
| 2e39A | 1 | 0.9067 | 5.6 | 0.923 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)