| d3jq3a1 |
| ID: | 1448506736 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (81) | ||
| Sequences: | 455 (248.9) | ||
| Seq/Len: | 5.617 | ||
| Nf(neff/√len): | 27.7 |
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: 5.617).
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 |
| 30_R | 72_E | 3.178 | 1.00 |
| 59_L | 73_L | 2.554 | 1.00 |
| 18_V | 21_R | 2.369 | 1.00 |
| 22_H | 80_E | 2.064 | 1.00 |
| 43_D | 47_Q | 1.942 | 1.00 |
| 40_V | 45_V | 1.935 | 1.00 |
| 25_F | 29_Q | 1.821 | 1.00 |
| 79_N | 86_G | 1.763 | 1.00 |
| 48_P | 60_I | 1.584 | 0.99 |
| 59_L | 77_V | 1.561 | 0.99 |
| 40_V | 66_S | 1.465 | 0.99 |
| 47_Q | 51_D | 1.461 | 0.99 |
| 62_G | 66_S | 1.371 | 0.98 |
| 18_V | 22_H | 1.366 | 0.98 |
| 31_L | 42_V | 1.364 | 0.97 |
| 45_V | 62_G | 1.341 | 0.97 |
| 48_P | 55_N | 1.314 | 0.97 |
| 36_T | 63_D | 1.273 | 0.96 |
| 31_L | 34_K | 1.262 | 0.95 |
| 40_V | 62_G | 1.235 | 0.95 |
| 29_Q | 32_F | 1.223 | 0.94 |
| 7_A | 12_Y | 1.209 | 0.94 |
| 21_R | 55_N | 1.185 | 0.93 |
| 37_A | 69_V | 1.185 | 0.93 |
| 54_G | 81_K | 1.180 | 0.93 |
| 72_E | 76_A | 1.171 | 0.93 |
| 9_F | 12_Y | 1.160 | 0.92 |
| 58_G | 61_A | 1.158 | 0.92 |
| 46_I | 50_V | 1.156 | 0.92 |
| 26_E | 29_Q | 1.153 | 0.92 |
| 31_L | 73_L | 1.139 | 0.91 |
| 18_V | 80_E | 1.121 | 0.90 |
| 18_V | 55_N | 1.120 | 0.90 |
| 55_N | 60_I | 1.112 | 0.90 |
| 48_P | 54_G | 1.097 | 0.89 |
| 71_K | 87_P | 1.094 | 0.89 |
| 28_Y | 51_D | 1.091 | 0.89 |
| 26_E | 30_R | 1.078 | 0.88 |
| 68_E | 71_K | 1.077 | 0.88 |
| 71_K | 75_D | 1.071 | 0.87 |
| 38_H | 53_F | 1.059 | 0.87 |
| 30_R | 34_K | 1.052 | 0.86 |
| 37_A | 65_E | 1.039 | 0.85 |
| 49_S | 57_I | 1.026 | 0.84 |
| 64_E | 85_F | 1.015 | 0.83 |
| 21_R | 80_E | 1.013 | 0.83 |
| 67_Y | 78_I | 1.006 | 0.82 |
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 | |
| 3jpzA | 2 | 1 | 100 | -0.002 | Contact Map |
| 3ju5A | 4 | 1 | 100 | 0.013 | Contact Map |
| 1qh4A | 4 | 1 | 100 | 0.021 | Contact Map |
| 1m15A | 1 | 1 | 100 | 0.024 | Contact Map |
| 4z9mA | 8 | 0 | 100 | 0.024 | Contact Map |
| 3l2fA | 18 | 0.9885 | 100 | 0.035 | Contact Map |
| 4wodA | 1 | 0.9885 | 100 | 0.057 | Contact Map |
| 4rf6A | 2 | 1 | 100 | 0.073 | Contact Map |
| 4xk8G | 2 | 0 | 7 | 0.929 | Contact Map |
| 5aj3g | 1 | 0 | 6.4 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)