| wieslaw |
| ID: | 1427832418 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 42 (42) | ||
| Sequences: | 123 (103.7) | ||
| Seq/Len: | 2.929 | ||
| Nf(neff/√len): | 16.0 |
HHblits Results: (2013_03)
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: 2.929).
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 |
| 8_I | 29_V | 2.690 | 1.00 |
| 5_A | 26_V | 2.496 | 1.00 |
| 18_L | 39_I | 2.492 | 1.00 |
| 13_R | 34_E | 2.483 | 1.00 |
| 3_N | 24_N | 2.164 | 1.00 |
| 10_T | 31_G | 1.942 | 0.99 |
| 16_V | 37_V | 1.443 | 0.94 |
| 4_S | 7_D | 1.436 | 0.94 |
| 17_Q | 38_L | 1.406 | 0.93 |
| 14_A | 35_S | 1.350 | 0.91 |
| 6_K | 27_E | 1.330 | 0.90 |
| 14_A | 37_V | 1.251 | 0.86 |
| 6_K | 32_K | 1.146 | 0.78 |
| 24_N | 41_N | 1.096 | 0.74 |
| 9_R | 30_V | 1.079 | 0.72 |
| 3_N | 20_N | 1.042 | 0.69 |
| 29_V | 35_S | 1.040 | 0.68 |
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 | |
| 2kj3A | 3 | 1 | 96.7 | 0.298 | Contact Map |
| 3h09A | 2 | 1 | 4.8 | 0.774 | Contact Map |
| 3syjA | 1 | 0.9762 | 2.2 | 0.81 | Contact Map |
| 4ce4E | 1 | 1 | 1.9 | 0.817 | Contact Map |
| 1wxrA | 1 | 0.9286 | 1.8 | 0.82 | Contact Map |
| 3ebhA | 1 | 1 | 1.4 | 0.829 | Contact Map |
| 4om9A | 1 | 0.9286 | 1.3 | 0.834 | Contact Map |
| 2yy5A | 4 | 0.881 | 1.2 | 0.836 | Contact Map |
| 3j7yE | 1 | 1 | 1.1 | 0.842 | Contact Map |
| 2mkiA | 1 | 0.4762 | 1 | 0.845 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)