| BUB1_CDI 5-36 4-26 |
| ID: | 1469272928 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 23 (19) | ||
| Sequences: | 83 (36.2) | ||
| Seq/Len: | 4.368 | ||
| Nf(neff/√len): | 8.3 |
Jackhmmer Results: (2016_04)
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: 4.368).
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 |
| 14_F | 20_Q | 1.737 | 0.99 |
| 6_V | 13_G | 1.720 | 0.99 |
| 18_M | 21_A | 1.638 | 0.99 |
| 16_M | 19_F | 1.615 | 0.99 |
| 7_H | 14_F | 1.558 | 0.99 |
| 7_H | 17_N | 1.535 | 0.98 |
| 6_V | 17_N | 1.433 | 0.97 |
| 12_L | 20_Q | 1.384 | 0.96 |
| 15_I | 20_Q | 1.315 | 0.95 |
| 13_G | 19_F | 1.297 | 0.94 |
| 9_K | 21_A | 1.071 | 0.82 |
| 9_K | 15_I | 1.058 | 0.81 |
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 | |
| 3lm3A | 1 | 1 | 8.7 | 0.8 | Contact Map |
| 3zdlB | 1 | 0.4348 | 8.5 | 0.8 | Contact Map |
| 4gmoA | 1 | 1 | 8 | 0.802 | Contact Map |
| 1pprM | 3 | 1 | 6 | 0.813 | Contact Map |
| 2c9eA | 1 | 1 | 5.2 | 0.818 | Contact Map |
| 3oakC | 2 | 0.913 | 4.8 | 0.821 | Contact Map |
| 3j21D | 1 | 0.8696 | 4.4 | 0.825 | Contact Map |
| 3iisM | 1 | 1 | 4.3 | 0.826 | Contact Map |
| 3j4aA | 12 | 1 | 4 | 0.828 | Contact Map |
| 4dkjA | 1 | 0.8261 | 3.7 | 0.832 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)