| cyt52 |
| ID: | 1678997837 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 134 (125) | ||
| Sequences: | 859 (515.8) | ||
| Seq/Len: | 6.872 | ||
| Nf(neff/√len): | 46.1 |
HHblits Results: (2016_02)
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 |
| 33_K | 80_I | 3.718 | 1.00 |
| 17_I | 29_I | 3.439 | 1.00 |
| 26_T | 41_L | 3.206 | 1.00 |
| 64_E | 73_R | 3.133 | 1.00 |
| 80_I | 83_E | 2.693 | 1.00 |
| 20_H | 25_S | 2.683 | 1.00 |
| 28_L | 37_L | 2.550 | 1.00 |
| 14_L | 29_I | 2.465 | 1.00 |
| 20_H | 27_W | 2.402 | 1.00 |
| 14_L | 87_D | 2.324 | 1.00 |
| 24_K | 38_T | 2.289 | 1.00 |
| 16_E | 19_K | 2.105 | 1.00 |
| 31_H | 64_E | 1.914 | 1.00 |
| 25_S | 38_T | 1.829 | 1.00 |
| 120_A | 124_A | 1.774 | 1.00 |
| 48_E | 65_D | 1.656 | 1.00 |
| 11_Y | 85_H | 1.641 | 1.00 |
| 17_I | 84_L | 1.557 | 1.00 |
| 15_E | 19_K | 1.517 | 0.99 |
| 75_M | 79_F | 1.453 | 0.99 |
| 42_E | 48_E | 1.411 | 0.99 |
| 85_H | 88_D | 1.400 | 0.99 |
| 64_E | 70_T | 1.389 | 0.99 |
| 26_T | 37_L | 1.385 | 0.99 |
| 50_V | 65_D | 1.362 | 0.98 |
| 74_E | 77_K | 1.341 | 0.98 |
| 69_S | 72_A | 1.297 | 0.98 |
| 113_W | 116_P | 1.295 | 0.98 |
| 10_K | 16_E | 1.274 | 0.97 |
| 12_Y | 17_I | 1.244 | 0.97 |
| 37_L | 41_L | 1.172 | 0.95 |
| 13_T | 16_E | 1.171 | 0.95 |
| 14_L | 85_H | 1.156 | 0.94 |
| 22_H | 25_S | 1.136 | 0.94 |
| 18_Q | 21_N | 1.129 | 0.93 |
| 14_L | 84_L | 1.058 | 0.90 |
| 58_D | 90_P | 1.057 | 0.90 |
| 70_T | 74_E | 1.056 | 0.90 |
| 27_W | 60_T | 1.044 | 0.89 |
| 49_E | 66_V | 1.042 | 0.89 |
| 42_E | 91_K | 1.041 | 0.89 |
| 26_T | 51_L | 1.023 | 0.88 |
| 41_L | 52_R | 1.013 | 0.87 |
| 35_Y | 61_E | 1.010 | 0.87 |
| 15_E | 22_H | 1.005 | 0.87 |
| 9_V | 80_I | 1.000 | 0.86 |
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 | |
| 1hkoA | 1 | 0.7761 | 100 | 0.387 | Contact Map |
| 4zr0A | 2 | 0 | 100 | 0.391 | Contact Map |
| 2keoA | 1 | 0.6866 | 100 | 0.399 | Contact Map |
| 1soxA | 2 | 0.8955 | 100 | 0.401 | Contact Map |
| 2ibjA | 1 | 0.6418 | 100 | 0.41 | Contact Map |
| 1cxyA | 1 | 0.5746 | 100 | 0.411 | Contact Map |
| 4hilA | 2 | 0.6343 | 100 | 0.415 | Contact Map |
| 3lf5A | 2 | 0.6493 | 100 | 0.423 | Contact Map |
| 3x34A | 1 | 0 | 99.9 | 0.434 | Contact Map |
| 1kbiA | 2 | 0.9776 | 99.9 | 0.434 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)