| trilo3 |
| ID: | 1490001742 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 42 (40) | ||
| Sequences: | 49 (46) | ||
| Seq/Len: | 1.225 | ||
| Nf(neff/√len): | 7.3 |
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: 1.225).
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 |
| 21_Q | 30_Q | 2.204 | 0.99 |
| 7_N | 31_F | 2.170 | 0.98 |
| 8_F | 17_A | 1.742 | 0.92 |
| 6_S | 41_T | 1.721 | 0.91 |
| 29_K | 33_G | 1.686 | 0.90 |
| 14_Y | 21_Q | 1.449 | 0.79 |
| 23_N | 30_Q | 1.365 | 0.73 |
| 33_G | 36_F | 1.325 | 0.69 |
| 20_T | 34_S | 1.302 | 0.67 |
| 19_G | 28_G | 1.276 | 0.65 |
| 9_G | 27_N | 1.220 | 0.60 |
| 31_F | 36_F | 1.209 | 0.59 |
| 33_G | 38_G | 1.198 | 0.58 |
| 4_S | 7_N | 1.179 | 0.56 |
| 12_T | 24_V | 1.160 | 0.54 |
| 17_A | 32_I | 1.126 | 0.51 |
| 26_G | 36_F | 1.090 | 0.47 |
| 12_T | 25_T | 1.072 | 0.46 |
| 11_G | 14_Y | 1.054 | 0.44 |
| 35_T | 38_G | 1.050 | 0.44 |
| 18_G | 27_N | 1.031 | 0.42 |
| 25_T | 41_T | 1.016 | 0.40 |
| 20_T | 37_Q | 1.006 | 0.39 |
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 | |
| 3rlfF | 1 | 1 | 1.4 | 0.862 | Contact Map |
| 3fewX | 1 | 0 | 1.3 | 0.867 | Contact Map |
| 2wq4A | 3 | 0.0952 | 1 | 0.875 | Contact Map |
| 3kogA | 1 | 0.1905 | 0.6 | 0.892 | Contact Map |
| 4c7lA | 2 | 0.6667 | 0.5 | 0.898 | Contact Map |
| 3cl5A | 1 | 0.6667 | 0.5 | 0.9 | Contact Map |
| 2jxfA | 1 | 0.4762 | 0.5 | 0.9 | Contact Map |
| 4j94A | 1 | 1 | 0.4 | 0.903 | Contact Map |
| 2b6nA | 1 | 1 | 0.4 | 0.905 | Contact Map |
| 4ecnA | 1 | 0.1905 | 0.4 | 0.907 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)