| 3lbw |
| ID: | 1508767901 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 23 (23) | ||
| Sequences: | 38 (5.7) | ||
| Seq/Len: | 1.652 | ||
| Nf(neff/√len): | 1.2 |
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: 1.652).
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 |
| 9_I | 21_R | 3.608 | 1.00 |
| 4_V | 8_I | 3.024 | 1.00 |
| 5_A | 9_I | 2.135 | 0.99 |
| 12_L | 19_L | 2.042 | 0.99 |
| 10_A | 23_X | 1.803 | 0.96 |
| 12_L | 15_I | 1.608 | 0.92 |
| 12_L | 18_I | 1.512 | 0.89 |
| 2_L | 7_S | 1.483 | 0.87 |
| 14_L | 22_L | 1.261 | 0.73 |
| 15_I | 22_L | 1.209 | 0.68 |
| 3_V | 7_S | 1.169 | 0.64 |
| 1_P | 4_V | 1.073 | 0.54 |
| 7_S | 10_A | 1.024 | 0.49 |
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 | |
| 2kihA | 4 | 1 | 99 | -0.016 | Contact Map |
| 3bkdA | 8 | 0.9565 | 98.9 | 0.014 | Contact Map |
| 3lbwA | 4 | 0.9565 | 98.9 | 0.017 | Contact Map |
| 2ljbA | 4 | 1 | 98.9 | 0.029 | Contact Map |
| 3vziA | 2 | 0.9565 | 6.3 | 0.799 | Contact Map |
| 2d0bA | 1 | 0.9565 | 5.1 | 0.808 | Contact Map |
| 3vzhA | 1 | 1 | 4.6 | 0.812 | Contact Map |
| 3j32A | 2 | 1 | 4.5 | 0.814 | Contact Map |
| 1afoA | 2 | 1 | 3.9 | 0.818 | Contact Map |
| 3vn5A | 1 | 0.9565 | 3.8 | 0.819 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)