| all_no_filtering |
| ID: | 1394221761 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 113 (112) | ||
| Sequences: | 1972 (1175.9) | ||
| Seq/Len: | 17.607 | ||
| Nf(neff/√len): | 111.1 |
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: 17.607).
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 |
| 40_D | 43_Q | 4.296 | 1.00 |
| 66_E | 74_A | 3.163 | 1.00 |
| 56_I | 73_V | 2.979 | 1.00 |
| 75_Y | 84_A | 2.866 | 1.00 |
| 66_E | 70_N | 2.801 | 1.00 |
| 38_I | 109_G | 2.595 | 1.00 |
| 77_N | 80_L | 2.562 | 1.00 |
| 41_K | 44_E | 2.394 | 1.00 |
| 76_A | 80_L | 2.348 | 1.00 |
| 4_T | 20_A | 2.295 | 1.00 |
| 32_I | 36_L | 2.219 | 1.00 |
| 27_I | 36_L | 1.962 | 1.00 |
| 4_T | 10_S | 1.929 | 1.00 |
| 9_F | 49_Y | 1.849 | 1.00 |
| 38_I | 47_K | 1.825 | 1.00 |
| 23_F | 26_L | 1.778 | 1.00 |
| 60_L | 63_S | 1.729 | 1.00 |
| 2_T | 34_S | 1.716 | 1.00 |
| 53_S | 65_Q | 1.647 | 1.00 |
| 6_Y | 35_S | 1.583 | 1.00 |
| 58_G | 75_Y | 1.544 | 1.00 |
| 12_I | 20_A | 1.537 | 1.00 |
| 93_E | 97_S | 1.503 | 1.00 |
| 1_G | 29_L | 1.478 | 1.00 |
| 16_I | 84_A | 1.418 | 1.00 |
| 58_G | 81_I | 1.353 | 0.99 |
| 25_A | 29_L | 1.340 | 0.99 |
| 70_N | 74_A | 1.314 | 0.99 |
| 59_V | 66_E | 1.312 | 0.99 |
| 59_V | 74_A | 1.306 | 0.99 |
| 80_L | 83_A | 1.270 | 0.99 |
| 86_Q | 91_A | 1.267 | 0.99 |
| 13_G | 16_I | 1.260 | 0.99 |
| 3_D | 60_L | 1.198 | 0.98 |
| 104_F | 107_G | 1.166 | 0.97 |
| 31_A | 110_V | 1.165 | 0.97 |
| 78_Q | 81_I | 1.126 | 0.97 |
| 22_D | 25_A | 1.111 | 0.96 |
| 26_L | 29_L | 1.110 | 0.96 |
| 23_F | 36_L | 1.100 | 0.96 |
| 38_I | 43_Q | 1.093 | 0.96 |
| 21_S | 26_L | 1.089 | 0.96 |
| 10_S | 34_S | 1.088 | 0.96 |
| 10_S | 20_A | 1.060 | 0.95 |
| 61_Q | 76_A | 1.050 | 0.94 |
| 58_G | 84_A | 1.047 | 0.94 |
| 3_D | 10_S | 1.016 | 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 | |
| 1wdnA | 1 | 0.9912 | 98.8 | 0.624 | Contact Map |
| 4oenA | 2 | 0.9912 | 98.4 | 0.67 | Contact Map |
| 1pb7A | 1 | 0.9292 | 98.1 | 0.69 | Contact Map |
| 2rc8A | 2 | 0.9912 | 98 | 0.701 | Contact Map |
| 1yaeA | 6 | 0.9823 | 97.7 | 0.72 | Contact Map |
| 3vv5A | 2 | 1 | 97.5 | 0.73 | Contact Map |
| 3i6vA | 1 | 0.9912 | 97.5 | 0.733 | Contact Map |
| 2ylnA | 1 | 1 | 97.4 | 0.738 | Contact Map |
| 4dz1A | 1 | 1 | 97.2 | 0.743 | Contact Map |
| 3g3kA | 2 | 0.9823 | 97.2 | 0.743 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)