| 2hp8 |
| ID: | 1494940538 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 68 (63) | ||
| Sequences: | 121 (61.3) | ||
| Seq/Len: | 1.921 | ||
| Nf(neff/√len): | 7.7 |
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: 1.921).
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 |
| 12_C | 15_Q | 3.255 | 1.00 |
| 31_V | 40_A | 2.065 | 0.99 |
| 29_Q | 49_V | 1.796 | 0.97 |
| 5_D | 8_Q | 1.638 | 0.95 |
| 10_Q | 37_K | 1.604 | 0.94 |
| 59_E | 62_T | 1.587 | 0.93 |
| 35_L | 49_V | 1.585 | 0.93 |
| 58_E | 61_L | 1.503 | 0.91 |
| 5_D | 53_F | 1.430 | 0.87 |
| 16_K | 52_G | 1.391 | 0.85 |
| 3_Q | 26_S | 1.390 | 0.85 |
| 30_A | 46_R | 1.376 | 0.85 |
| 59_E | 63_R | 1.354 | 0.83 |
| 8_Q | 47_S | 1.319 | 0.81 |
| 54_E | 57_E | 1.284 | 0.79 |
| 46_R | 53_F | 1.264 | 0.77 |
| 58_E | 62_T | 1.249 | 0.76 |
| 8_Q | 19_Q | 1.233 | 0.75 |
| 6_P | 34_E | 1.232 | 0.74 |
| 58_E | 63_R | 1.226 | 0.74 |
| 36_R | 51_S | 1.136 | 0.66 |
| 5_D | 19_Q | 1.131 | 0.65 |
| 24_M | 33_Q | 1.102 | 0.62 |
| 60_N | 63_R | 1.093 | 0.61 |
| 5_D | 52_G | 1.070 | 0.59 |
| 32_I | 40_A | 1.066 | 0.58 |
| 14_I | 22_S | 1.065 | 0.58 |
| 45_G | 57_E | 1.061 | 0.58 |
| 29_Q | 58_E | 1.057 | 0.57 |
| 8_Q | 41_Q | 1.049 | 0.56 |
| 4_K | 22_S | 1.017 | 0.53 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1hp8A | 1 | 1 | 99.8 | 0.254 | Contact Map |
| 1ei0A | 1 | 0.5588 | 98.8 | 0.573 | Contact Map |
| 2lqtA | 1 | 0.9265 | 90.9 | 0.798 | Contact Map |
| 5aj3m | 1 | 0 | 84.4 | 0.819 | Contact Map |
| 2lqlA | 1 | 0.6176 | 2.8 | 0.924 | Contact Map |
| 2l0yB | 1 | 0.3088 | 2 | 0.929 | Contact Map |
| 4ntwC | 1 | 0.4118 | 1.4 | 0.935 | Contact Map |
| 3v9mA | 2 | 0.4265 | 1.2 | 0.937 | Contact Map |
| 4bv4R | 1 | 0.6765 | 1.1 | 0.939 | Contact Map |
| 2i9wA | 1 | 0.3382 | 1.1 | 0.939 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)