| brca2 |
| ID: | 1517368517 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 35 (35) | ||
| Sequences: | 95 (37.5) | ||
| Seq/Len: | 2.714 | ||
| Nf(neff/√len): | 6.3 |
HHblits Results: (2016_02)
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: 2.714).
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 |
| 20_K | 26_V | 2.218 | 1.00 |
| 21_E | 27_K | 1.891 | 0.99 |
| 5_L | 27_K | 1.662 | 0.98 |
| 5_L | 16_V | 1.640 | 0.97 |
| 24_D | 31_D | 1.613 | 0.97 |
| 3_P | 31_D | 1.532 | 0.95 |
| 1_K | 18_I | 1.472 | 0.94 |
| 2_E | 22_S | 1.356 | 0.90 |
| 15_K | 23_L | 1.293 | 0.87 |
| 18_I | 23_L | 1.292 | 0.87 |
| 10_T | 26_V | 1.288 | 0.87 |
| 12_S | 26_V | 1.249 | 0.84 |
| 9_H | 28_N | 1.215 | 0.82 |
| 10_T | 15_K | 1.158 | 0.78 |
| 19_A | 33_K | 1.134 | 0.75 |
| 1_K | 9_H | 1.051 | 0.67 |
| 2_E | 26_V | 1.016 | 0.63 |
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 | |
| 1n0wB | 1 | 0.9429 | 99.5 | 0.115 | Contact Map |
| 2mtnA | 1 | 0.5429 | 29.9 | 0.809 | Contact Map |
| 4mfkA | 1 | 1 | 15.2 | 0.833 | Contact Map |
| 2zjrR | 1 | 0.7143 | 11.2 | 0.843 | Contact Map |
| 4tp9U | 1 | 0.7429 | 11.1 | 0.843 | Contact Map |
| 3bboW | 1 | 0.7714 | 10.3 | 0.846 | Contact Map |
| 4g06A | 2 | 0.9429 | 10.3 | 0.846 | Contact Map |
| 4rb6Y | 1 | 0.6857 | 9.2 | 0.849 | Contact Map |
| 2zjrC | 1 | 0.8 | 8.9 | 0.849 | Contact Map |
| 3terA | 2 | 0.8286 | 6.9 | 0.857 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)