| 2RQL |
| ID: | 1447167185 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 95 (95) | ||
| Sequences: | 2784 (1811.4) | ||
| Seq/Len: | 29.305 | ||
| Nf(neff/√len): | 185.8 |
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: 29.305).
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 |
| 67_G | 73_A | 4.116 | 1.00 |
| 7_G | 12_I | 2.581 | 1.00 |
| 14_E | 18_E | 2.563 | 1.00 |
| 52_A | 77_L | 2.408 | 1.00 |
| 86_T | 90_D | 2.086 | 1.00 |
| 50_S | 73_A | 1.967 | 1.00 |
| 41_L | 50_S | 1.837 | 1.00 |
| 20_V | 41_L | 1.837 | 1.00 |
| 17_R | 21_T | 1.762 | 1.00 |
| 49_T | 66_E | 1.758 | 1.00 |
| 16_L | 70_M | 1.729 | 1.00 |
| 37_V | 54_L | 1.630 | 1.00 |
| 5_I | 20_V | 1.624 | 1.00 |
| 18_E | 22_A | 1.621 | 1.00 |
| 43_V | 48_H | 1.613 | 1.00 |
| 65_A | 76_G | 1.572 | 1.00 |
| 51_D | 64_S | 1.515 | 1.00 |
| 19_F | 74_I | 1.512 | 1.00 |
| 6_T | 38_Y | 1.457 | 1.00 |
| 30_Y | 82_A | 1.440 | 1.00 |
| 63_A | 84_Q | 1.435 | 1.00 |
| 49_T | 64_S | 1.352 | 0.99 |
| 53_T | 62_H | 1.333 | 0.99 |
| 15_A | 71_Y | 1.307 | 0.99 |
| 54_L | 81_L | 1.294 | 0.99 |
| 7_G | 10_V | 1.268 | 0.99 |
| 56_V | 85_L | 1.266 | 0.99 |
| 41_L | 70_M | 1.261 | 0.99 |
| 13_T | 16_L | 1.251 | 0.99 |
| 24_F | 52_A | 1.247 | 0.99 |
| 53_T | 60_E | 1.243 | 0.98 |
| 13_T | 71_Y | 1.236 | 0.98 |
| 48_H | 70_M | 1.235 | 0.98 |
| 83_R | 87_K | 1.204 | 0.98 |
| 12_I | 17_R | 1.195 | 0.98 |
| 69_D | 72_A | 1.193 | 0.98 |
| 52_A | 81_L | 1.177 | 0.98 |
| 65_A | 80_K | 1.153 | 0.97 |
| 70_M | 74_I | 1.149 | 0.97 |
| 44_E | 49_T | 1.142 | 0.97 |
| 8_N | 42_K | 1.117 | 0.96 |
| 22_A | 25_A | 1.108 | 0.96 |
| 6_T | 40_V | 1.101 | 0.96 |
| 31_F | 92_L | 1.096 | 0.96 |
| 16_L | 41_L | 1.093 | 0.96 |
| 7_G | 13_T | 1.052 | 0.95 |
| 65_A | 77_L | 1.044 | 0.94 |
| 14_E | 17_R | 1.036 | 0.94 |
| 5_I | 21_T | 1.025 | 0.93 |
| 76_G | 80_K | 1.019 | 0.93 |
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 | |
| 3v2cY | 1 | 0.9895 | 99.9 | -0.021 | Contact Map |
| 3v26X | 1 | 1 | 99.9 | -0.013 | Contact Map |
| 4heiA | 2 | 0.9684 | 99.9 | -0.008 | Contact Map |
| 1imuA | 1 | 1 | 99.9 | -0.007 | Contact Map |
| 3tqmA | 4 | 0.9789 | 99.9 | -0.007 | Contact Map |
| 2ywqA | 4 | 0.9158 | 99.9 | 0.023 | Contact Map |
| 4iwxA | 1 | 0.8211 | 24.6 | 0.865 | Contact Map |
| 3r84A | 12 | 0.7368 | 17.7 | 0.874 | Contact Map |
| 3ku7A | 2 | 0.5684 | 16.7 | 0.875 | Contact Map |
| 3vpbA | 4 | 0.8421 | 16.4 | 0.876 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)