| rand304 |
| ID: | 1478453309 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 92 (92) | ||
| Sequences: | 500 (500) | ||
| Seq/Len: | 5.435 | ||
| Nf(neff/√len): | 52.1 |
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: 5.435).
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_F | 39_A | 1.651 | 0.99 |
| 39_A | 85_I | 1.533 | 0.99 |
| 26_Q | 40_Y | 1.502 | 0.99 |
| 3_N | 72_K | 1.443 | 0.98 |
| 77_N | 88_V | 1.436 | 0.98 |
| 14_E | 46_W | 1.427 | 0.98 |
| 8_V | 45_Q | 1.405 | 0.98 |
| 26_Q | 67_K | 1.364 | 0.97 |
| 16_C | 92_D | 1.349 | 0.97 |
| 21_E | 28_F | 1.319 | 0.97 |
| 27_L | 66_A | 1.278 | 0.96 |
| 44_G | 62_W | 1.247 | 0.95 |
| 55_K | 84_R | 1.233 | 0.94 |
| 17_I | 21_E | 1.226 | 0.94 |
| 62_W | 71_I | 1.218 | 0.94 |
| 30_Y | 41_I | 1.216 | 0.94 |
| 41_I | 51_K | 1.214 | 0.94 |
| 5_D | 54_H | 1.213 | 0.94 |
| 3_N | 44_G | 1.205 | 0.93 |
| 40_Y | 47_S | 1.201 | 0.93 |
| 38_R | 74_I | 1.198 | 0.93 |
| 28_F | 39_A | 1.192 | 0.93 |
| 50_I | 56_W | 1.188 | 0.93 |
| 20_P | 34_C | 1.182 | 0.93 |
| 54_H | 84_R | 1.179 | 0.92 |
| 39_A | 48_W | 1.176 | 0.92 |
| 18_P | 33_E | 1.160 | 0.92 |
| 9_A | 83_S | 1.147 | 0.91 |
| 14_E | 56_W | 1.136 | 0.90 |
| 10_L | 39_A | 1.135 | 0.90 |
| 43_S | 48_W | 1.134 | 0.90 |
| 55_K | 75_L | 1.127 | 0.90 |
| 10_L | 31_T | 1.098 | 0.88 |
| 19_R | 80_V | 1.095 | 0.88 |
| 11_Q | 90_C | 1.085 | 0.88 |
| 30_Y | 79_L | 1.075 | 0.87 |
| 2_I | 72_K | 1.075 | 0.87 |
| 20_P | 79_L | 1.066 | 0.86 |
| 33_E | 37_R | 1.065 | 0.86 |
| 45_Q | 62_W | 1.063 | 0.86 |
| 42_G | 46_W | 1.056 | 0.86 |
| 35_N | 91_V | 1.043 | 0.85 |
| 32_N | 40_Y | 1.041 | 0.85 |
| 20_P | 86_K | 1.039 | 0.84 |
| 22_W | 25_L | 1.037 | 0.84 |
| 5_D | 34_C | 1.033 | 0.84 |
| 88_V | 92_D | 1.018 | 0.83 |
| 74_I | 80_V | 1.016 | 0.83 |
| 48_W | 71_I | 1.013 | 0.82 |
| 77_N | 85_I | 1.011 | 0.82 |
| 21_E | 27_L | 1.011 | 0.82 |
| 63_V | 83_S | 1.010 | 0.82 |
| 46_W | 68_P | 1.007 | 0.82 |
| 18_P | 47_S | 1.003 | 0.81 |
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 | |
| 1qysA | 1 | 1 | 0.4 | 0.889 | Contact Map |
| 2mcfA | 1 | 0.5652 | 0.3 | 0.904 | Contact Map |
| 1rm1C | 1 | 0.5109 | 0.3 | 0.91 | Contact Map |
| 2exuA | 1 | 0.4348 | 0.2 | 0.913 | Contact Map |
| 1pyaA | 3 | 0.4891 | 0.2 | 0.915 | Contact Map |
| 1nvpC | 1 | 0.5 | 0.2 | 0.915 | Contact Map |
| 2w2sA | 1 | 0.337 | 0.2 | 0.916 | Contact Map |
| 1nh2C | 1 | 0.5 | 0.2 | 0.917 | Contact Map |
| 1kqrA | 1 | 0.413 | 0.2 | 0.92 | Contact Map |
| 2aenA | 8 | 0.413 | 0.2 | 0.92 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)