| tesy |
| ID: | 1490003882 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 39 (39) | ||
| Sequences: | 48 (44) | ||
| Seq/Len: | 1.231 | ||
| Nf(neff/√len): | 7.0 |
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: 1.231).
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 |
| 30_G | 35_G | 1.993 | 0.97 |
| 4_Y | 38_H | 1.949 | 0.96 |
| 18_V | 27_Q | 1.802 | 0.94 |
| 5_N | 28_L | 1.759 | 0.93 |
| 11_V | 18_V | 1.669 | 0.90 |
| 16_G | 25_G | 1.526 | 0.83 |
| 9_D | 22_K | 1.503 | 0.82 |
| 32_T | 35_G | 1.478 | 0.81 |
| 17_T | 34_L | 1.374 | 0.73 |
| 26_N | 34_L | 1.371 | 0.73 |
| 6_Y | 14_P | 1.358 | 0.72 |
| 26_N | 30_G | 1.297 | 0.67 |
| 14_P | 29_P | 1.230 | 0.61 |
| 14_P | 39_F | 1.221 | 0.60 |
| 23_G | 33_F | 1.218 | 0.60 |
| 11_V | 22_K | 1.158 | 0.54 |
| 5_N | 37_V | 1.133 | 0.52 |
| 2_S | 5_N | 1.130 | 0.51 |
| 3_F | 10_Q | 1.126 | 0.51 |
| 17_T | 31_A | 1.114 | 0.50 |
| 11_V | 15_G | 1.043 | 0.43 |
| 20_T | 27_Q | 1.038 | 0.42 |
| 30_G | 33_F | 1.029 | 0.42 |
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 | |
| 3zxsA | 3 | 0.7179 | 0.6 | 0.886 | Contact Map |
| 1gff3 | 1 | 0.2821 | 0.5 | 0.888 | Contact Map |
| 1m06J | 1 | 0.2821 | 0.5 | 0.888 | Contact Map |
| 3fewX | 1 | 0 | 0.4 | 0.899 | Contact Map |
| 4mzdA | 1 | 1 | 0.4 | 0.901 | Contact Map |
| 4qniA | 1 | 0.1795 | 0.4 | 0.902 | Contact Map |
| 4qq0A | 1 | 0 | 0.4 | 0.903 | Contact Map |
| 4uypA | 2 | 0.5897 | 0.4 | 0.903 | Contact Map |
| 2cclA | 2 | 0.5897 | 0.4 | 0.903 | Contact Map |
| 3nqkA | 1 | 0.1282 | 0.4 | 0.904 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)