| alignment_402b_A2 |
| ID: | 1448909852 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 36 (33) | ||
| Sequences: | 40 (10.3) | ||
| Seq/Len: | 1.212 | ||
| Nf(neff/√len): | 1.8 |
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: 1.212).
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 |
| 7_T | 19_D | 3.056 | 1.00 |
| 9_T | 12_S | 1.742 | 0.92 |
| 7_T | 34_L | 1.494 | 0.81 |
| 8_D | 31_T | 1.378 | 0.73 |
| 2_V | 16_K | 1.378 | 0.73 |
| 17_D | 31_T | 1.347 | 0.71 |
| 1_R | 23_I | 1.306 | 0.67 |
| 20_S | 25_G | 1.261 | 0.63 |
| 23_I | 35_S | 1.251 | 0.63 |
| 5_S | 25_G | 1.217 | 0.59 |
| 8_D | 33_S | 1.154 | 0.53 |
| 21_S | 35_S | 1.150 | 0.53 |
| 9_T | 17_D | 1.135 | 0.51 |
| 5_S | 20_S | 1.109 | 0.49 |
| 2_V | 23_I | 1.107 | 0.49 |
| 20_S | 28_A | 1.065 | 0.45 |
| 11_S | 20_S | 1.060 | 0.44 |
| 6_D | 11_S | 1.052 | 0.43 |
| 17_D | 34_L | 1.003 | 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 | |
| 2ofkA | 2 | 0.9167 | 2.5 | 0.89 | Contact Map |
| 2jg6A | 1 | 0.9167 | 2.4 | 0.892 | Contact Map |
| 4ixjA | 2 | 0.9167 | 2.2 | 0.894 | Contact Map |
| 4e29A | 2 | 0.1389 | 1.2 | 0.908 | Contact Map |
| 3l0iB | 2 | 0 | 1.2 | 0.909 | Contact Map |
| 3urhA | 2 | 0 | 1.1 | 0.911 | Contact Map |
| 3wx6A | 2 | 0.5278 | 1.1 | 0.911 | Contact Map |
| 2oxgY | 4 | 0.2778 | 1.1 | 0.911 | Contact Map |
| 4cbhA | 4 | 0 | 1 | 0.913 | Contact Map |
| 1i24A | 1 | 0.1944 | 1 | 0.913 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)