| d3rbxf2 |
| ID: | 1448773147 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 90 (76) | ||
| Sequences: | 5213 (3837.8) | ||
| Seq/Len: | 68.592 | ||
| Nf(neff/√len): | 440.2 |
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: 68.592).
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 |
| 54_R | 72_D | 3.959 | 1.00 |
| 25_I | 68_F | 3.316 | 1.00 |
| 36_V | 49_I | 2.706 | 1.00 |
| 54_R | 69_R | 2.401 | 1.00 |
| 34_V | 38_D | 2.253 | 1.00 |
| 19_R | 80_P | 2.247 | 1.00 |
| 40_D | 43_D | 2.050 | 1.00 |
| 23_V | 76_G | 2.015 | 1.00 |
| 52_V | 66_Y | 1.989 | 1.00 |
| 79_K | 82_E | 1.933 | 1.00 |
| 78_G | 83_I | 1.859 | 1.00 |
| 42_H | 48_I | 1.797 | 1.00 |
| 22_E | 73_I | 1.783 | 1.00 |
| 35_S | 38_D | 1.781 | 1.00 |
| 31_L | 39_A | 1.728 | 1.00 |
| 32_E | 70_A | 1.675 | 1.00 |
| 46_G | 82_E | 1.617 | 1.00 |
| 52_V | 72_D | 1.612 | 1.00 |
| 50_I | 77_I | 1.599 | 1.00 |
| 69_R | 72_D | 1.540 | 1.00 |
| 68_F | 74_I | 1.523 | 1.00 |
| 54_R | 66_Y | 1.428 | 1.00 |
| 82_E | 85_R | 1.383 | 0.99 |
| 45_T | 89_Y | 1.284 | 0.99 |
| 51_G | 75_L | 1.269 | 0.99 |
| 35_S | 67_S | 1.237 | 0.98 |
| 49_I | 76_G | 1.222 | 0.98 |
| 18_R | 77_I | 1.203 | 0.98 |
| 33_G | 69_R | 1.197 | 0.98 |
| 36_V | 68_F | 1.196 | 0.98 |
| 47_V | 78_G | 1.135 | 0.97 |
| 54_R | 59_I | 1.110 | 0.96 |
| 53_G | 75_L | 1.104 | 0.96 |
| 29_S | 32_E | 1.024 | 0.93 |
| 24_P | 73_I | 1.002 | 0.92 |
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 | |
| 2aefA | 2 | 1 | 99.2 | 0.173 | Contact Map |
| 1lnqA | 8 | 1 | 99.2 | 0.176 | Contact Map |
| 4xttA | 2 | 0 | 99 | 0.234 | Contact Map |
| 1vctA | 1 | 0.9889 | 99 | 0.245 | Contact Map |
| 4g65A | 2 | 0.9556 | 98.9 | 0.267 | Contact Map |
| 4gx0A | 4 | 0.9444 | 98.9 | 0.281 | Contact Map |
| 3jxoA | 2 | 0.9222 | 98.9 | 0.291 | Contact Map |
| 3l4bC | 4 | 0.9222 | 98.8 | 0.303 | Contact Map |
| 3mt5A | 1 | 0.9556 | 98.7 | 0.317 | Contact Map |
| 3nafA | 1 | 0.9667 | 98.7 | 0.338 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)