| 2dk7 |
| ID: | 1444054909 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 73 (66) | ||
| Sequences: | 159 (99.1) | ||
| Seq/Len: | 2.409 | ||
| Nf(neff/√len): | 12.2 |
HHblits Results: (2015_06)
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: 2.409).
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 |
| 50_L | 54_A | 2.474 | 1.00 |
| 34_F | 37_P | 1.689 | 0.97 |
| 16_P | 58_K | 1.646 | 0.97 |
| 21_P | 31_R | 1.579 | 0.95 |
| 9_A | 31_R | 1.577 | 0.95 |
| 59_I | 62_E | 1.558 | 0.95 |
| 59_I | 67_K | 1.554 | 0.95 |
| 5_S | 70_P | 1.397 | 0.90 |
| 50_L | 60_I | 1.301 | 0.85 |
| 11_P | 21_P | 1.299 | 0.85 |
| 40_R | 56_V | 1.283 | 0.84 |
| 10_K | 51_I | 1.278 | 0.84 |
| 65_H | 68_S | 1.276 | 0.83 |
| 65_H | 69_G | 1.268 | 0.83 |
| 26_W | 64_P | 1.266 | 0.83 |
| 30_E | 66_K | 1.257 | 0.82 |
| 14_T | 43_M | 1.244 | 0.81 |
| 8_K | 40_R | 1.171 | 0.75 |
| 35_Y | 59_I | 1.167 | 0.75 |
| 7_G | 14_T | 1.149 | 0.73 |
| 62_E | 67_K | 1.140 | 0.73 |
| 28_G | 34_F | 1.138 | 0.72 |
| 12_V | 28_G | 1.125 | 0.71 |
| 58_K | 61_Q | 1.119 | 0.71 |
| 38_T | 65_H | 1.098 | 0.69 |
| 51_I | 59_I | 1.083 | 0.67 |
| 22_W | 27_T | 1.071 | 0.66 |
| 7_G | 10_K | 1.058 | 0.64 |
| 27_T | 33_F | 1.054 | 0.64 |
| 32_V | 60_I | 1.049 | 0.63 |
| 17_I | 59_I | 1.044 | 0.63 |
| 29_D | 37_P | 1.032 | 0.62 |
| 31_R | 48_D | 1.030 | 0.61 |
| 21_P | 25_V | 1.027 | 0.61 |
| 62_E | 68_S | 1.022 | 0.60 |
| 25_V | 29_D | 1.020 | 0.60 |
| 45_D | 50_L | 1.020 | 0.60 |
| 19_G | 22_W | 1.015 | 0.60 |
| 30_E | 68_S | 1.011 | 0.59 |
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 | |
| 2dk7A | 1 | 1 | 99.7 | 0.363 | Contact Map |
| 1e0lA | 1 | 0.5068 | 97.6 | 0.72 | Contact Map |
| 2dk1A | 1 | 0.6849 | 97.4 | 0.728 | Contact Map |
| 2l5fA | 1 | 0.7397 | 97.1 | 0.742 | Contact Map |
| 2jxwA | 1 | 0.6301 | 96.7 | 0.756 | Contact Map |
| 4rohA | 1 | 0.6849 | 96.6 | 0.76 | Contact Map |
| 1o6wA | 1 | 0.726 | 96.3 | 0.765 | Contact Map |
| 2ysiA | 1 | 0.5479 | 96.3 | 0.766 | Contact Map |
| 1ywiA | 1 | 0.3836 | 96.2 | 0.768 | Contact Map |
| 2kxqA | 1 | 0.6986 | 96.2 | 0.768 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)