| test2 |
| ID: | 1447067821 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 60 (60) | ||
| Sequences: | 529 (307.2) | ||
| Seq/Len: | 8.817 | ||
| Nf(neff/√len): | 39.7 |
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: 8.817).
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_F | 14_L | 2.797 | 1.00 |
| 7_K | 53_A | 2.534 | 1.00 |
| 33_I | 38_Y | 2.223 | 1.00 |
| 16_E | 37_R | 2.132 | 1.00 |
| 41_L | 50_A | 2.110 | 1.00 |
| 29_M | 38_Y | 1.996 | 1.00 |
| 29_M | 33_I | 1.988 | 1.00 |
| 11_K | 53_A | 1.977 | 1.00 |
| 43_K | 46_E | 1.901 | 1.00 |
| 28_A | 31_M | 1.804 | 1.00 |
| 15_K | 54_Y | 1.764 | 1.00 |
| 4_E | 8_Q | 1.470 | 1.00 |
| 19_V | 23_A | 1.444 | 0.99 |
| 2_T | 5_E | 1.402 | 0.99 |
| 13_L | 32_I | 1.315 | 0.99 |
| 25_W | 45_S | 1.272 | 0.98 |
| 24_S | 38_Y | 1.248 | 0.98 |
| 12_E | 16_E | 1.219 | 0.98 |
| 23_A | 28_A | 1.182 | 0.97 |
| 2_T | 18_R | 1.103 | 0.95 |
| 25_W | 39_S | 1.101 | 0.95 |
| 41_L | 49_Q | 1.098 | 0.95 |
| 25_W | 30_K | 1.008 | 0.91 |
| 28_A | 51_F | 1.001 | 0.91 |
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 | |
| 1uzcA | 1 | 1 | 99.7 | 0.022 | Contact Map |
| 2b7eA | 1 | 0.95 | 99.7 | 0.029 | Contact Map |
| 2dodA | 1 | 0.9833 | 99.7 | 0.031 | Contact Map |
| 2jucA | 1 | 0.9167 | 99.7 | 0.088 | Contact Map |
| 3hfhA | 2 | 0.8667 | 99.6 | 0.101 | Contact Map |
| 2doeA | 1 | 1 | 99.5 | 0.188 | Contact Map |
| 4fqgA | 2 | 1 | 99.3 | 0.248 | Contact Map |
| 2cqnA | 1 | 1 | 98.6 | 0.441 | Contact Map |
| 2dofA | 1 | 1 | 97.5 | 0.58 | Contact Map |
| 2kfdA | 1 | 0.95 | 83.9 | 0.749 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)