| HS-bho-c |
| ID: | 1483026899 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 91 (73) | ||
| Sequences: | 115 (85.1) | ||
| Seq/Len: | 1.575 | ||
| Nf(neff/√len): | 10.0 |
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: 1.575).
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 |
| 11_Y | 23_D | 2.717 | 1.00 |
| 16_E | 19_Q | 2.350 | 1.00 |
| 16_E | 20_K | 2.078 | 0.99 |
| 34_I | 46_M | 2.029 | 0.98 |
| 34_I | 42_A | 1.882 | 0.97 |
| 58_N | 61_A | 1.772 | 0.95 |
| 11_Y | 19_Q | 1.746 | 0.95 |
| 29_M | 33_A | 1.672 | 0.93 |
| 28_Q | 32_D | 1.577 | 0.90 |
| 45_H | 48_R | 1.557 | 0.90 |
| 18_L | 33_A | 1.534 | 0.89 |
| 47_Q | 50_I | 1.424 | 0.83 |
| 18_L | 21_C | 1.310 | 0.75 |
| 63_E | 70_A | 1.298 | 0.74 |
| 25_K | 39_P | 1.275 | 0.72 |
| 44_Y | 48_R | 1.272 | 0.72 |
| 1_G | 41_D | 1.262 | 0.71 |
| 42_A | 46_M | 1.239 | 0.69 |
| 1_G | 42_A | 1.237 | 0.69 |
| 59_S | 62_S | 1.233 | 0.69 |
| 25_K | 28_Q | 1.219 | 0.68 |
| 7_P | 52_S | 1.190 | 0.65 |
| 1_G | 46_M | 1.188 | 0.65 |
| 46_M | 50_I | 1.186 | 0.64 |
| 39_P | 43_K | 1.173 | 0.63 |
| 11_Y | 38_D | 1.167 | 0.63 |
| 17_E | 36_K | 1.165 | 0.62 |
| 8_V | 41_D | 1.137 | 0.60 |
| 13_S | 63_E | 1.126 | 0.59 |
| 63_E | 67_G | 1.098 | 0.56 |
| 20_K | 31_Q | 1.086 | 0.54 |
| 14_L | 49_C | 1.062 | 0.52 |
| 18_L | 38_D | 1.057 | 0.51 |
| 1_G | 5_L | 1.048 | 0.50 |
| 24_V | 39_P | 1.046 | 0.50 |
| 31_Q | 34_I | 1.044 | 0.50 |
| 1_G | 8_V | 1.014 | 0.47 |
| 16_E | 32_D | 1.002 | 0.46 |
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 | |
| 1us7B | 1 | 0.5824 | 100 | 0.172 | Contact Map |
| 2kwvA | 1 | 0.3407 | 48.8 | 0.897 | Contact Map |
| 2mbbA | 1 | 0.3626 | 35.3 | 0.906 | Contact Map |
| 4bm5A | 1 | 0.7033 | 19.8 | 0.916 | Contact Map |
| 3ai4A | 1 | 0.2857 | 19.7 | 0.917 | Contact Map |
| 4mdaA | 1 | 0.5714 | 15.8 | 0.92 | Contact Map |
| 2khuA | 1 | 0.3187 | 15.8 | 0.92 | Contact Map |
| 4umkA | 4 | 0 | 15.1 | 0.921 | Contact Map |
| 2hpgA | 4 | 0.967 | 12.4 | 0.924 | Contact Map |
| 2bw2A | 1 | 0.4615 | 11.2 | 0.925 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)