| BUB1_CDI 12-35 |
| ID: | 1419351476 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 24 (21) | ||
| Sequences: | 49 (17.6) | ||
| Seq/Len: | 2.333 | ||
| Nf(neff/√len): | 3.8 |
Jackhmmer Results: (2014_04_16)
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: 2.333).
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_V | 14_G | 4.268 | 1.00 |
| 19_M | 22_A | 2.156 | 1.00 |
| 13_L | 19_M | 2.112 | 1.00 |
| 7_V | 16_I | 1.850 | 0.99 |
| 11_E | 19_M | 1.678 | 0.97 |
| 18_N | 21_Q | 1.396 | 0.89 |
| 8_H | 18_N | 1.376 | 0.88 |
| 16_I | 21_Q | 1.376 | 0.88 |
| 13_L | 22_A | 1.366 | 0.88 |
| 8_H | 12_A | 1.359 | 0.88 |
| 8_H | 21_Q | 1.192 | 0.76 |
| 11_E | 22_A | 1.152 | 0.73 |
| 7_V | 13_L | 1.084 | 0.66 |
| 9_T | 13_L | 1.044 | 0.62 |
| 9_T | 18_N | 1.041 | 0.62 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | 0.4167 | 9.7 | 0.801 | Contact Map |
| 3oakC | 2 | 0.875 | 9 | 0.804 | Contact Map |
| 3lm3A | 1 | 1 | 8 | 0.809 | Contact Map |
| 3zf7r | 1 | 1 | 7.9 | 0.809 | Contact Map |
| 3j21D | 1 | 0.875 | 7.7 | 0.81 | Contact Map |
| 3iz5D | 1 | 0.8333 | 5.6 | 0.822 | Contact Map |
| 1vwxC | 1 | 1 | 5.6 | 0.822 | Contact Map |
| 4gmoA | 1 | 1 | 5.5 | 0.823 | Contact Map |
| 2c9eA | 1 | 1 | 4.9 | 0.827 | Contact Map |
| 4a17C | 1 | 1 | 4.8 | 0.827 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)