| O6K |
| ID: | 1487704882 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 72 (68) | ||
| Sequences: | 433 (278.3) | ||
| Seq/Len: | 6.368 | ||
| Nf(neff/√len): | 33.7 |
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: 6.368).
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 |
| 34_D | 39_I | 3.765 | 1.00 |
| 7_V | 24_I | 3.339 | 1.00 |
| 17_K | 60_L | 2.113 | 1.00 |
| 34_D | 40_L | 1.831 | 1.00 |
| 38_N | 42_D | 1.831 | 1.00 |
| 20_L | 24_I | 1.764 | 1.00 |
| 12_G | 18_G | 1.743 | 1.00 |
| 34_D | 61_Y | 1.584 | 0.99 |
| 6_F | 63_E | 1.557 | 0.99 |
| 19_R | 23_E | 1.482 | 0.99 |
| 11_R | 25_F | 1.467 | 0.99 |
| 35_D | 68_L | 1.379 | 0.98 |
| 37_F | 46_T | 1.303 | 0.97 |
| 47_H | 51_T | 1.287 | 0.97 |
| 1_Y | 68_L | 1.286 | 0.97 |
| 37_F | 44_I | 1.286 | 0.97 |
| 14_H | 18_G | 1.249 | 0.96 |
| 40_L | 61_Y | 1.245 | 0.96 |
| 20_L | 50_F | 1.238 | 0.96 |
| 1_Y | 6_F | 1.223 | 0.96 |
| 7_V | 20_L | 1.210 | 0.95 |
| 10_V | 63_E | 1.200 | 0.95 |
| 17_K | 63_E | 1.184 | 0.94 |
| 20_L | 51_T | 1.170 | 0.94 |
| 41_S | 45_E | 1.146 | 0.93 |
| 9_T | 25_F | 1.137 | 0.93 |
| 41_S | 58_D | 1.112 | 0.92 |
| 1_Y | 5_Q | 1.060 | 0.89 |
| 15_D | 18_G | 1.055 | 0.89 |
| 13_R | 22_E | 1.044 | 0.88 |
| 35_D | 63_E | 1.016 | 0.86 |
| 6_F | 10_V | 1.010 | 0.85 |
| 42_D | 46_T | 1.002 | 0.85 |
| 17_K | 44_I | 1.000 | 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 | |
| 2o6kA | 2 | 1 | 99.9 | 0.06 | Contact Map |
| 2fj6A | 1 | 1 | 99.9 | 0.108 | Contact Map |
| 2kvsA | 1 | 0.9583 | 99.8 | 0.208 | Contact Map |
| 3i5pA | 1 | 0.7083 | 27.1 | 0.876 | Contact Map |
| 3oiiA | 2 | 0.8889 | 9.8 | 0.899 | Contact Map |
| 3vtxA | 2 | 0.5972 | 5.8 | 0.909 | Contact Map |
| 2hh6A | 1 | 0.9583 | 5.6 | 0.91 | Contact Map |
| 4zuzA | 2 | 0 | 4.3 | 0.914 | Contact Map |
| 3wvzA | 2 | 0.4444 | 3.9 | 0.916 | Contact Map |
| 1elrA | 1 | 0.5833 | 3.6 | 0.917 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)