| BPT1_BOVIN_corrected |
| ID: | 1394362160 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 0% gaps before running GREMLIN. |
| Length: | 53 (53) | ||
| Sequences: | 1749 (1412.3) | ||
| Seq/Len: | 33.000 | ||
| Nf(neff/√len): | 194.0 |
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: 33.000).
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 |
| 11_C | 35_C | 6.185 | 1.00 |
| 21_N | 28_Q | 3.416 | 1.00 |
| 17_R | 41_N | 3.291 | 1.00 |
| 45_A | 49_M | 3.134 | 1.00 |
| 24_A | 28_Q | 2.554 | 1.00 |
| 6_P | 19_F | 2.111 | 1.00 |
| 17_R | 43_K | 1.931 | 1.00 |
| 44_S | 47_D | 1.723 | 1.00 |
| 18_Y | 45_A | 1.691 | 1.00 |
| 14_R | 31_V | 1.688 | 1.00 |
| 1_F | 51_T | 1.464 | 1.00 |
| 38_K | 41_N | 1.318 | 0.99 |
| 4_E | 42_F | 1.260 | 0.99 |
| 9_G | 37_A | 1.257 | 0.99 |
| 32_Y | 37_A | 1.255 | 0.99 |
| 4_E | 39_R | 1.251 | 0.99 |
| 10_P | 36_R | 1.183 | 0.98 |
| 43_K | 47_D | 1.182 | 0.98 |
| 16_I | 29_T | 1.168 | 0.97 |
| 47_D | 50_R | 1.136 | 0.97 |
| 19_F | 28_Q | 1.057 | 0.95 |
| 49_M | 53_G | 1.051 | 0.94 |
| 16_I | 31_V | 1.027 | 0.94 |
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 | |
| 2ddiA | 1 | 1 | 99.4 | -0.016 | Contact Map |
| 4dtgK | 1 | 1 | 99.4 | -0.01 | Contact Map |
| 1co7I | 1 | 0.7736 | 99.4 | -0.005 | Contact Map |
| 1yc0I | 1 | 1 | 99.3 | 0.006 | Contact Map |
| 4bqdA | 2 | 1 | 99.3 | 0.008 | Contact Map |
| 1adzA | 1 | 1 | 99.3 | 0.016 | Contact Map |
| 1dtkA | 1 | 1 | 99.3 | 0.018 | Contact Map |
| 1jc6A | 1 | 1 | 99.3 | 0.019 | Contact Map |
| 3augA | 2 | 1 | 99.3 | 0.019 | Contact Map |
| 3m7qB | 1 | 1 | 99.3 | 0.02 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)