| Ex01_4WYQ_chB |
| ID: | 1475105481 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 75 (74) | ||
| Sequences: | 185 (122.2) | ||
| Seq/Len: | 2.500 | ||
| Nf(neff/√len): | 14.2 |
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: 2.500).
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 |
| 21_V | 41_L | 2.358 | 1.00 |
| 19_F | 23_Y | 1.664 | 0.97 |
| 15_E | 55_T | 1.493 | 0.94 |
| 38_L | 48_V | 1.367 | 0.89 |
| 25_D | 60_R | 1.338 | 0.88 |
| 7_C | 57_E | 1.324 | 0.87 |
| 26_I | 59_A | 1.290 | 0.85 |
| 70_Y | 73_I | 1.276 | 0.84 |
| 52_S | 74_M | 1.255 | 0.83 |
| 14_S | 60_R | 1.248 | 0.82 |
| 25_D | 50_H | 1.232 | 0.81 |
| 63_A | 68_L | 1.212 | 0.80 |
| 40_E | 44_Q | 1.207 | 0.79 |
| 37_C | 70_Y | 1.202 | 0.79 |
| 7_C | 18_A | 1.202 | 0.79 |
| 62_E | 66_R | 1.198 | 0.79 |
| 39_V | 56_R | 1.174 | 0.77 |
| 70_Y | 74_M | 1.162 | 0.76 |
| 30_S | 41_L | 1.161 | 0.76 |
| 33_G | 70_Y | 1.158 | 0.75 |
| 2_L | 6_C | 1.152 | 0.75 |
| 8_R | 12_E | 1.135 | 0.73 |
| 38_L | 49_C | 1.133 | 0.73 |
| 3_G | 18_A | 1.130 | 0.73 |
| 29_L | 34_L | 1.118 | 0.72 |
| 34_L | 56_R | 1.105 | 0.70 |
| 54_T | 62_E | 1.104 | 0.70 |
| 10_L | 14_S | 1.088 | 0.69 |
| 65_R | 69_Q | 1.085 | 0.68 |
| 3_G | 50_H | 1.065 | 0.66 |
| 9_V | 12_E | 1.059 | 0.66 |
| 18_A | 54_T | 1.052 | 0.65 |
| 46_A | 74_M | 1.043 | 0.64 |
| 32_S | 54_T | 1.034 | 0.63 |
| 34_L | 52_S | 1.034 | 0.63 |
| 38_L | 42_S | 1.029 | 0.62 |
| 51_G | 64_A | 1.019 | 0.61 |
| 31_L | 73_I | 1.015 | 0.61 |
| 40_E | 47_T | 1.008 | 0.60 |
| 2_L | 58_A | 1.005 | 0.60 |
| 5_A | 57_E | 1.001 | 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 | |
| 4dkkA | 1 | 0.9733 | 99.8 | 0.094 | Contact Map |
| 4wyqB | 2 | 1 | 99.7 | 0.189 | Contact Map |
| 1ekzA | 1 | 0.9467 | 94.6 | 0.735 | Contact Map |
| 3n3wA | 2 | 0 | 94 | 0.743 | Contact Map |
| 1whqA | 1 | 0.9733 | 93.5 | 0.748 | Contact Map |
| 4oogC | 1 | 0.9867 | 93.3 | 0.749 | Contact Map |
| 1qu6A | 1 | 0.9733 | 93.1 | 0.751 | Contact Map |
| 1x47A | 1 | 0.9733 | 93 | 0.752 | Contact Map |
| 1x48A | 1 | 0.96 | 92.9 | 0.753 | Contact Map |
| 3llhA | 2 | 0.8667 | 92.9 | 0.753 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)