| d2wbka5 |
| ID: | 1448374193 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 81 (80) | ||
| Sequences: | 373 (294) | ||
| Seq/Len: | 4.662 | ||
| Nf(neff/√len): | 32.9 |
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: 4.662).
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 |
| 27_A | 30_I | 4.303 | 1.00 |
| 39_A | 58_I | 3.911 | 1.00 |
| 28_K | 47_D | 2.589 | 1.00 |
| 75_H | 78_E | 2.289 | 1.00 |
| 32_I | 41_Y | 2.177 | 1.00 |
| 31_F | 45_F | 1.654 | 0.99 |
| 29_D | 47_D | 1.439 | 0.98 |
| 30_I | 46_F | 1.433 | 0.97 |
| 20_T | 55_K | 1.431 | 0.97 |
| 6_V | 21_L | 1.429 | 0.97 |
| 5_S | 16_K | 1.416 | 0.97 |
| 7_S | 12_Q | 1.333 | 0.96 |
| 9_Q | 12_Q | 1.303 | 0.95 |
| 29_D | 39_A | 1.300 | 0.95 |
| 41_Y | 44_N | 1.299 | 0.95 |
| 32_I | 56_V | 1.288 | 0.94 |
| 31_F | 44_N | 1.269 | 0.94 |
| 11_K | 15_G | 1.267 | 0.94 |
| 26_L | 47_D | 1.218 | 0.92 |
| 5_S | 9_Q | 1.215 | 0.92 |
| 41_Y | 46_F | 1.211 | 0.92 |
| 7_S | 10_M | 1.118 | 0.87 |
| 18_E | 55_K | 1.117 | 0.87 |
| 67_E | 71_V | 1.115 | 0.87 |
| 7_S | 14_D | 1.095 | 0.85 |
| 2_P | 15_G | 1.094 | 0.85 |
| 46_F | 56_V | 1.082 | 0.84 |
| 42_S | 46_F | 1.073 | 0.84 |
| 34_T | 38_G | 1.050 | 0.82 |
| 48_L | 54_K | 1.034 | 0.80 |
| 41_Y | 75_H | 1.033 | 0.80 |
| 4_T | 7_S | 1.028 | 0.80 |
| 3_P | 6_V | 1.024 | 0.80 |
| 7_S | 80_Y | 1.011 | 0.78 |
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 | |
| 2je8A | 2 | 1 | 99.6 | 0.165 | Contact Map |
| 4cvuA | 1 | 0.9877 | 99.4 | 0.248 | Contact Map |
| 2vzsA | 2 | 1 | 98.8 | 0.436 | Contact Map |
| 3sbqA | 2 | 0.8148 | 3.8 | 0.892 | Contact Map |
| 2i9iA | 1 | 0.963 | 3.8 | 0.892 | Contact Map |
| 3gnfB | 1 | 0.8765 | 3.7 | 0.893 | Contact Map |
| 4m6tA | 1 | 0.6667 | 3.1 | 0.897 | Contact Map |
| 1jovA | 1 | 0.6543 | 2.9 | 0.898 | Contact Map |
| 4o5jA | 1 | 0.1111 | 2.9 | 0.898 | Contact Map |
| 4gioA | 2 | 0.8889 | 2.8 | 0.899 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)