| pku |
| ID: | 1440494136 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 80 (67) | ||
| Sequences: | 2193 (1311.1) | ||
| Seq/Len: | 32.731 | ||
| Nf(neff/√len): | 160.2 |
HHblits Results: (2015_06)
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: 32.731).
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 |
| 21_F | 63_T | 3.225 | 1.00 |
| 31_A | 35_R | 2.791 | 1.00 |
| 40_N | 75_S | 2.656 | 1.00 |
| 18_S | 64_Y | 2.585 | 1.00 |
| 35_R | 39_E | 2.496 | 1.00 |
| 43_N | 66_D | 2.241 | 1.00 |
| 65_L | 73_L | 2.185 | 1.00 |
| 26_E | 32_K | 1.853 | 1.00 |
| 52_S | 60_E | 1.840 | 1.00 |
| 23_L | 29_A | 1.812 | 1.00 |
| 19_L | 65_L | 1.800 | 1.00 |
| 12_N | 15_G | 1.723 | 1.00 |
| 32_K | 38_E | 1.671 | 1.00 |
| 67_K | 73_L | 1.666 | 1.00 |
| 51_P | 59_Y | 1.646 | 1.00 |
| 15_G | 68_R | 1.539 | 1.00 |
| 51_P | 57_D | 1.407 | 0.99 |
| 21_F | 33_V | 1.339 | 0.99 |
| 25_E | 43_N | 1.276 | 0.99 |
| 37_F | 44_L | 1.251 | 0.99 |
| 37_F | 76_I | 1.229 | 0.98 |
| 18_S | 62_F | 1.202 | 0.98 |
| 30_L | 47_I | 1.194 | 0.98 |
| 44_L | 65_L | 1.163 | 0.97 |
| 68_R | 71_P | 1.137 | 0.97 |
| 12_N | 68_R | 1.105 | 0.96 |
| 48_E | 64_Y | 1.091 | 0.96 |
| 25_E | 58_E | 1.083 | 0.96 |
| 67_K | 71_P | 1.071 | 0.95 |
| 17_I | 67_K | 1.022 | 0.93 |
| 28_G | 43_N | 1.021 | 0.93 |
| 23_L | 33_V | 1.018 | 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
- 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 | |
| 1phzA | 1 | 1 | 99.8 | 0.018 | Contact Map |
| 4lubA | 2 | 0.9875 | 99.8 | 0.076 | Contact Map |
| 2qmxA | 2 | 1 | 99.8 | 0.082 | Contact Map |
| 2mdaA | 2 | 0.9875 | 99.7 | 0.091 | Contact Map |
| 3mwbA | 2 | 0.975 | 99.7 | 0.101 | Contact Map |
| 2qmwA | 2 | 0.95 | 99.7 | 0.115 | Contact Map |
| 3luyA | 1 | 1 | 99.7 | 0.152 | Contact Map |
| 2ko1A | 2 | 0.825 | 96.2 | 0.673 | Contact Map |
| 2lvwA | 2 | 0.8875 | 95.3 | 0.696 | Contact Map |
| 1y7pA | 3 | 0.8125 | 94.8 | 0.704 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)