| BUB1_CD |
| ID: | 1469452275 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 20 (20) | ||
| Sequences: | 70 (23.9) | ||
| Seq/Len: | 3.500 | ||
| Nf(neff/√len): | 5.3 |
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: 3.500).
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 |
| 15_M | 20_L | 1.897 | 1.00 |
| 4_N | 11_D | 1.681 | 0.99 |
| 3_I | 10_D | 1.641 | 0.98 |
| 3_I | 9_M | 1.584 | 0.98 |
| 11_D | 17_Q | 1.497 | 0.97 |
| 13_N | 16_F | 1.448 | 0.96 |
| 17_Q | 20_L | 1.385 | 0.94 |
| 15_M | 18_K | 1.385 | 0.94 |
| 4_N | 14_S | 1.353 | 0.93 |
| 5_L | 20_L | 1.295 | 0.91 |
| 14_S | 18_K | 1.252 | 0.89 |
| 5_L | 11_D | 1.113 | 0.80 |
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 | |
| 3zdlB | 1 | 0.5 | 24.3 | 0.709 | Contact Map |
| 4w8pB | 1 | 0.6 | 8.6 | 0.763 | Contact Map |
| 2c9eA | 1 | 1 | 7.6 | 0.769 | Contact Map |
| 1hekA | 2 | 0.6 | 6.3 | 0.776 | Contact Map |
| 1pprM | 3 | 1 | 6.1 | 0.779 | Contact Map |
| 3lm3A | 1 | 1 | 5.4 | 0.783 | Contact Map |
| 1gpjA | 1 | 0.85 | 5.4 | 0.783 | Contact Map |
| 3iisM | 1 | 1 | 5.1 | 0.786 | Contact Map |
| 4rgwA | 1 | 1 | 5 | 0.787 | Contact Map |
| 4n7rA | 2 | 0.65 | 4.9 | 0.788 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)