| bHLH |
| ID: | 1482023283 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 53 (51) | ||
| Sequences: | 903 (400) | ||
| Seq/Len: | 17.706 | ||
| Nf(neff/√len): | 56.0 |
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: 17.706).
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 |
| 10_E | 13_R | 2.558 | 1.00 |
| 7_N | 11_R | 2.444 | 1.00 |
| 49_Y | 53_L | 2.005 | 1.00 |
| 50_I | 53_L | 1.978 | 1.00 |
| 3_V | 6_R | 1.976 | 1.00 |
| 46_A | 49_Y | 1.838 | 1.00 |
| 40_V | 44_R | 1.659 | 1.00 |
| 46_A | 50_I | 1.558 | 1.00 |
| 6_R | 14_V | 1.546 | 1.00 |
| 43_L | 46_A | 1.509 | 1.00 |
| 18_N | 40_V | 1.405 | 0.99 |
| 40_V | 45_S | 1.392 | 0.99 |
| 35_K | 38_S | 1.311 | 0.99 |
| 9_R | 13_R | 1.173 | 0.98 |
| 43_L | 53_L | 1.131 | 0.97 |
| 48_E | 52_A | 1.127 | 0.97 |
| 5_R | 21_F | 1.092 | 0.96 |
| 12_N | 15_K | 1.090 | 0.96 |
| 9_R | 14_V | 1.071 | 0.95 |
| 38_S | 41_E | 1.032 | 0.94 |
| 7_N | 14_V | 1.010 | 0.93 |
| 30_N | 37_M | 1.006 | 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 | |
| 2lfhA | 2 | 1 | 99.6 | 0.112 | Contact Map |
| 2ypaA | 1 | 1 | 99.5 | 0.166 | Contact Map |
| 4ayaA | 2 | 0.8679 | 99.5 | 0.166 | Contact Map |
| 2ypaB | 1 | 1 | 99.5 | 0.175 | Contact Map |
| 2ql2B | 2 | 1 | 99.4 | 0.2 | Contact Map |
| 1mdyA | 1 | 0.9811 | 99.3 | 0.243 | Contact Map |
| 3u5vA | 1 | 0.9057 | 99.1 | 0.313 | Contact Map |
| 1nkpA | 2 | 1 | 99 | 0.337 | Contact Map |
| 1nlwA | 2 | 0.9811 | 98.9 | 0.376 | Contact Map |
| 1hloA | 2 | 0.9811 | 98.8 | 0.401 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)