| BPTI |
| ID: | 1517905325 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 58 (56) | ||
| Sequences: | 4535 (3441.7) | ||
| Seq/Len: | 80.982 | ||
| Nf(neff/√len): | 459.9 |
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: 80.982).
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_C | 38_C | 3.880 | 1.00 |
| 9_P | 22_F | 3.153 | 1.00 |
| 48_A | 52_M | 3.096 | 1.00 |
| 24_N | 31_Q | 2.739 | 1.00 |
| 20_R | 44_N | 2.492 | 1.00 |
| 17_R | 34_V | 2.449 | 1.00 |
| 27_A | 31_Q | 2.437 | 1.00 |
| 20_R | 46_K | 1.920 | 1.00 |
| 4_F | 54_T | 1.868 | 1.00 |
| 47_S | 50_D | 1.836 | 1.00 |
| 13_P | 39_R | 1.831 | 1.00 |
| 21_Y | 48_A | 1.821 | 1.00 |
| 19_I | 32_T | 1.819 | 1.00 |
| 51_C | 55_C | 1.725 | 1.00 |
| 52_M | 56_G | 1.636 | 1.00 |
| 22_F | 31_Q | 1.558 | 1.00 |
| 7_E | 42_R | 1.537 | 1.00 |
| 6_L | 25_A | 1.512 | 1.00 |
| 19_I | 34_V | 1.475 | 1.00 |
| 49_E | 53_R | 1.226 | 0.98 |
| 46_K | 50_D | 1.222 | 0.98 |
| 28_G | 56_G | 1.151 | 0.97 |
| 41_K | 44_N | 1.085 | 0.96 |
| 7_E | 45_F | 1.049 | 0.94 |
| 17_R | 36_G | 1.020 | 0.93 |
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 | |
| 2ddiA | 1 | 1 | 99.1 | -0.188 | Contact Map |
| 1yc0I | 1 | 1 | 99.1 | -0.176 | Contact Map |
| 4bqdA | 2 | 1 | 99.1 | -0.176 | Contact Map |
| 1co7I | 1 | 0.7069 | 99.1 | -0.175 | Contact Map |
| 3aubA | 2 | 1 | 99.1 | -0.173 | Contact Map |
| 1g6xA | 1 | 1 | 99.1 | -0.173 | Contact Map |
| 1y62A | 6 | 0.9655 | 99.1 | -0.171 | Contact Map |
| 3augA | 2 | 1 | 99 | -0.168 | Contact Map |
| 1bf0A | 1 | 1 | 99 | -0.166 | Contact Map |
| 1jc6A | 1 | 1 | 99 | -0.162 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)