| d1yx7a_ |
| ID: | 1448773059 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 83 (71) | ||
| Sequences: | 5206 (3212.4) | ||
| Seq/Len: | 73.324 | ||
| Nf(neff/√len): | 381.2 |
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: 73.324).
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 |
| 23_Y | 65_K | 4.230 | 1.00 |
| 26_A | 52_A | 2.940 | 1.00 |
| 10_E | 68_K | 2.700 | 1.00 |
| 21_D | 28_E | 2.632 | 1.00 |
| 14_K | 20_G | 2.126 | 1.00 |
| 6_K | 72_L | 2.123 | 1.00 |
| 59_D | 62_S | 1.930 | 1.00 |
| 43_S | 46_K | 1.861 | 1.00 |
| 10_E | 14_K | 1.831 | 1.00 |
| 17_D | 22_G | 1.801 | 1.00 |
| 30_Q | 44_K | 1.734 | 1.00 |
| 18_A | 31_T | 1.638 | 1.00 |
| 67_S | 70_E | 1.598 | 1.00 |
| 21_D | 25_T | 1.596 | 1.00 |
| 26_A | 55_I | 1.560 | 1.00 |
| 59_D | 63_D | 1.533 | 1.00 |
| 63_D | 67_S | 1.521 | 1.00 |
| 61_N | 67_S | 1.411 | 1.00 |
| 8_E | 11_A | 1.381 | 0.99 |
| 16_L | 32_F | 1.379 | 0.99 |
| 58_A | 66_I | 1.336 | 0.99 |
| 63_D | 70_E | 1.328 | 0.99 |
| 58_A | 74_A | 1.285 | 0.99 |
| 59_D | 64_G | 1.260 | 0.99 |
| 19_N | 28_E | 1.173 | 0.98 |
| 30_Q | 34_V | 1.172 | 0.98 |
| 68_K | 72_L | 1.170 | 0.97 |
| 52_A | 56_K | 1.155 | 0.97 |
| 21_D | 65_K | 1.129 | 0.97 |
| 15_K | 35_T | 1.123 | 0.97 |
| 30_Q | 47_V | 1.102 | 0.96 |
| 17_D | 28_E | 1.092 | 0.96 |
| 75_N | 78_L | 1.075 | 0.95 |
| 23_Y | 67_S | 1.045 | 0.94 |
| 42_L | 47_V | 1.011 | 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 | |
| 1yx7A | 1 | 0.9759 | 99.1 | 0.179 | Contact Map |
| 4d1eA | 1 | 0.9277 | 99 | 0.194 | Contact Map |
| 3mwuA | 1 | 0.6506 | 98.9 | 0.227 | Contact Map |
| 2jjzA | 1 | 0.9277 | 98.9 | 0.228 | Contact Map |
| 2d58A | 1 | 0.9277 | 98.9 | 0.231 | Contact Map |
| 3u0kA | 1 | 0.8795 | 98.9 | 0.233 | Contact Map |
| 1c7vA | 1 | 0.8072 | 98.9 | 0.235 | Contact Map |
| 1wy9A | 1 | 0.9277 | 98.9 | 0.235 | Contact Map |
| 2lc5A | 1 | 0.9277 | 98.9 | 0.235 | Contact Map |
| 4il1A | 4 | 0 | 98.9 | 0.237 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)