| 806_6 |
| ID: | 1433406420 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 30 (30) | ||
| Sequences: | 171 (102.6) | ||
| Seq/Len: | 5.700 | ||
| Nf(neff/√len): | 18.7 |
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: 5.700).
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 |
| 5_I | 16_H | 1.926 | 1.00 |
| 27_N | 30_I | 1.611 | 0.99 |
| 5_I | 25_D | 1.606 | 0.99 |
| 22_E | 30_I | 1.579 | 0.99 |
| 7_D | 13_V | 1.528 | 0.99 |
| 24_V | 28_K | 1.459 | 0.99 |
| 7_D | 11_N | 1.360 | 0.97 |
| 5_I | 30_I | 1.252 | 0.95 |
| 2_P | 14_I | 1.193 | 0.94 |
| 21_G | 25_D | 1.182 | 0.93 |
| 19_E | 26_K | 1.163 | 0.92 |
| 4_L | 10_G | 1.151 | 0.92 |
| 24_V | 29_I | 1.120 | 0.90 |
| 21_G | 26_K | 1.096 | 0.89 |
| 4_L | 11_N | 1.090 | 0.89 |
| 14_I | 20_F | 1.027 | 0.84 |
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 | |
| 3gvoA | 1 | 1 | 98.2 | 0.317 | Contact Map |
| 3k62A | 1 | 1 | 97.9 | 0.368 | Contact Map |
| 3v71A | 1 | 1 | 97.8 | 0.381 | Contact Map |
| 3k49A | 3 | 1 | 97.7 | 0.402 | Contact Map |
| 4wzrA | 2 | 1 | 97.7 | 0.403 | Contact Map |
| 3bwtA | 1 | 1 | 96.4 | 0.504 | Contact Map |
| 2vldA | 2 | 0.9 | 8.7 | 0.817 | Contact Map |
| 3c0kA | 2 | 1 | 8.6 | 0.817 | Contact Map |
| 2b78A | 1 | 1 | 5.6 | 0.832 | Contact Map |
| 3mtvA | 1 | 1 | 4.6 | 0.838 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)