| 2LOL_A |
| ID: | 1416444770 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 81 (76) | ||
| Sequences: | 1725 (1050.3) | ||
| Seq/Len: | 22.697 | ||
| Nf(neff/√len): | 120.5 |
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: 22.697).
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 |
| 10_K | 53_E | 3.983 | 1.00 |
| 70_S | 74_K | 3.448 | 1.00 |
| 31_R | 34_E | 3.060 | 1.00 |
| 7_I | 77_K | 2.558 | 1.00 |
| 32_F | 72_V | 2.392 | 1.00 |
| 67_K | 71_D | 2.237 | 1.00 |
| 28_T | 70_S | 2.107 | 1.00 |
| 16_A | 23_K | 1.915 | 1.00 |
| 8_E | 12_I | 1.821 | 1.00 |
| 71_D | 74_K | 1.760 | 1.00 |
| 11_V | 50_I | 1.756 | 1.00 |
| 8_E | 28_T | 1.750 | 1.00 |
| 66_I | 72_V | 1.689 | 1.00 |
| 8_E | 73_I | 1.662 | 1.00 |
| 13_E | 23_K | 1.589 | 1.00 |
| 12_I | 23_K | 1.468 | 1.00 |
| 27_T | 30_S | 1.467 | 1.00 |
| 16_A | 26_I | 1.432 | 1.00 |
| 19_L | 38_A | 1.432 | 1.00 |
| 29_D | 70_S | 1.431 | 1.00 |
| 44_V | 48_M | 1.430 | 1.00 |
| 22_D | 25_I | 1.403 | 0.99 |
| 62_E | 79_R | 1.339 | 0.99 |
| 49_A | 52_V | 1.331 | 0.99 |
| 62_E | 75_Y | 1.279 | 0.99 |
| 26_I | 30_S | 1.275 | 0.99 |
| 44_V | 60_D | 1.268 | 0.99 |
| 74_K | 77_K | 1.253 | 0.99 |
| 9_Q | 13_E | 1.176 | 0.98 |
| 11_V | 73_I | 1.117 | 0.96 |
| 12_I | 16_A | 1.083 | 0.96 |
| 32_F | 43_T | 1.073 | 0.95 |
| 10_K | 54_Y | 1.073 | 0.95 |
| 26_I | 69_V | 1.042 | 0.94 |
| 38_A | 48_M | 1.027 | 0.94 |
| 58_I | 75_Y | 1.013 | 0.93 |
| 19_L | 46_L | 1.002 | 0.92 |
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 | |
| 2l9fA | 1 | 0.9753 | 99.5 | 0.265 | Contact Map |
| 2kciA | 1 | 0.9506 | 99.4 | 0.301 | Contact Map |
| 2lkiA | 1 | 0.9506 | 99.4 | 0.311 | Contact Map |
| 4bpfA | 1 | 0.9506 | 99.4 | 0.313 | Contact Map |
| 3ce7A | 1 | 0.9753 | 99.3 | 0.335 | Contact Map |
| 2kwlA | 1 | 0.9877 | 99.3 | 0.353 | Contact Map |
| 2cnrA | 1 | 0.9877 | 99.3 | 0.355 | Contact Map |
| 1x3oA | 1 | 0.9877 | 99.3 | 0.359 | Contact Map |
| 2l4bA | 1 | 0.9877 | 99.2 | 0.364 | Contact Map |
| 2qnwA | 1 | 0.9877 | 99.2 | 0.369 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)