| BamE |
| ID: | 1455804648 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 118 (107) | ||
| Sequences: | 973 (658.7) | ||
| Seq/Len: | 9.093 | ||
| Nf(neff/√len): | 63.7 |
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: 9.093).
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 |
| 93_I | 101_V | 4.850 | 1.00 |
| 40_Q | 44_D | 2.572 | 1.00 |
| 46_L | 101_V | 2.440 | 1.00 |
| 52_K | 99_G | 2.366 | 1.00 |
| 94_S | 103_D | 2.302 | 1.00 |
| 72_I | 94_S | 1.822 | 1.00 |
| 66_S | 69_G | 1.736 | 1.00 |
| 43_V | 91_Y | 1.713 | 1.00 |
| 46_L | 55_V | 1.687 | 1.00 |
| 39_T | 42_A | 1.683 | 1.00 |
| 33_N | 79_Q | 1.667 | 1.00 |
| 16_L | 19_G | 1.617 | 1.00 |
| 45_K | 58_I | 1.582 | 1.00 |
| 11_I | 14_S | 1.580 | 1.00 |
| 4_L | 7_I | 1.541 | 1.00 |
| 96_N | 102_A | 1.528 | 1.00 |
| 50_Q | 54_Q | 1.480 | 1.00 |
| 5_R | 8_I | 1.480 | 1.00 |
| 74_Y | 92_T | 1.475 | 1.00 |
| 55_V | 101_V | 1.425 | 0.99 |
| 59_M | 91_Y | 1.391 | 0.99 |
| 17_L | 20_C | 1.358 | 0.99 |
| 12_T | 15_F | 1.347 | 0.99 |
| 73_W | 95_F | 1.326 | 0.99 |
| 56_L | 61_S | 1.311 | 0.99 |
| 38_L | 42_A | 1.301 | 0.99 |
| 54_Q | 57_F | 1.272 | 0.98 |
| 78_R | 88_Q | 1.256 | 0.98 |
| 33_N | 37_Y | 1.229 | 0.98 |
| 14_S | 17_L | 1.211 | 0.98 |
| 46_L | 59_M | 1.196 | 0.97 |
| 38_L | 43_V | 1.167 | 0.97 |
| 38_L | 41_E | 1.124 | 0.96 |
| 54_Q | 74_Y | 1.123 | 0.96 |
| 91_Y | 104_I | 1.113 | 0.96 |
| 69_G | 72_I | 1.104 | 0.95 |
| 37_Y | 79_Q | 1.088 | 0.95 |
| 33_N | 77_F | 1.052 | 0.94 |
| 47_K | 50_Q | 1.042 | 0.93 |
| 51_T | 57_F | 1.038 | 0.93 |
| 21_S | 51_T | 1.037 | 0.93 |
| 27_V | 104_I | 1.035 | 0.93 |
| 51_T | 54_Q | 1.031 | 0.93 |
| 29_R | 106_R | 1.029 | 0.93 |
| 2_S | 5_R | 1.027 | 0.92 |
| 27_V | 30_P | 1.026 | 0.92 |
| 36_N | 59_M | 1.019 | 0.92 |
| 63_M | 77_F | 1.005 | 0.91 |
| 54_Q | 73_W | 1.003 | 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 | |
| 2pxgA | 1 | 0.7797 | 99.9 | 0.308 | Contact Map |
| 2km7A | 1 | 0.839 | 99.9 | 0.345 | Contact Map |
| 2yh9A | 3 | 0.5763 | 99.8 | 0.399 | Contact Map |
| 4dm5A | 4 | 0.7119 | 99.4 | 0.554 | Contact Map |
| 3d4eA | 1 | 0.7627 | 97.6 | 0.751 | Contact Map |
| 3gmxB | 2 | 0.661 | 97.1 | 0.771 | Contact Map |
| 3gmvX | 1 | 0.6695 | 97.1 | 0.774 | Contact Map |
| 3n4iB | 1 | 0.6525 | 97 | 0.777 | Contact Map |
| 4ygtA | 1 | 0.7458 | 92.8 | 0.829 | Contact Map |
| 3zbiC | 14 | 0.2373 | 87.3 | 0.848 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)