| BamE |
| ID: | 1429270450 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 113 (110) | ||
| Sequences: | 611 (444.1) | ||
| Seq/Len: | 5.555 | ||
| Nf(neff/√len): | 42.3 |
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: 5.555).
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_L | 101_L | 3.841 | 1.00 |
| 46_I | 101_L | 2.417 | 1.00 |
| 40_A | 44_S | 2.170 | 1.00 |
| 52_Q | 99_G | 2.029 | 1.00 |
| 66_D | 69_G | 1.923 | 1.00 |
| 54_Q | 57_Y | 1.809 | 1.00 |
| 45_K | 58_A | 1.787 | 1.00 |
| 46_I | 58_A | 1.759 | 1.00 |
| 94_T | 103_N | 1.735 | 1.00 |
| 50_M | 54_Q | 1.642 | 0.99 |
| 73_W | 95_F | 1.584 | 0.99 |
| 38_L | 43_V | 1.566 | 0.99 |
| 72_T | 94_T | 1.544 | 0.99 |
| 39_T | 42_D | 1.529 | 0.99 |
| 43_V | 91_L | 1.504 | 0.99 |
| 56_A | 61_T | 1.453 | 0.98 |
| 74_F | 92_T | 1.391 | 0.98 |
| 91_L | 104_I | 1.374 | 0.98 |
| 93_L | 104_I | 1.345 | 0.97 |
| 34_Q | 68_F | 1.308 | 0.96 |
| 39_T | 77_F | 1.295 | 0.96 |
| 28_Y | 62_P | 1.293 | 0.96 |
| 19_G | 22_T | 1.278 | 0.96 |
| 38_L | 42_D | 1.264 | 0.95 |
| 63_L | 77_F | 1.255 | 0.95 |
| 33_N | 77_F | 1.249 | 0.95 |
| 31_D | 79_Q | 1.247 | 0.95 |
| 29_R | 32_I | 1.240 | 0.95 |
| 21_S | 51_T | 1.223 | 0.94 |
| 69_G | 72_T | 1.212 | 0.94 |
| 51_T | 100_V | 1.196 | 0.93 |
| 32_I | 36_N | 1.187 | 0.93 |
| 47_R | 50_M | 1.166 | 0.92 |
| 19_G | 30_P | 1.163 | 0.92 |
| 36_N | 59_L | 1.158 | 0.92 |
| 2_R | 5_T | 1.136 | 0.91 |
| 39_T | 48_V | 1.112 | 0.90 |
| 17_T | 20_C | 1.109 | 0.89 |
| 43_V | 106_N | 1.085 | 0.88 |
| 67_P | 76_V | 1.073 | 0.87 |
| 45_K | 54_Q | 1.068 | 0.87 |
| 27_V | 67_P | 1.066 | 0.87 |
| 78_R | 88_Q | 1.060 | 0.86 |
| 55_V | 101_L | 1.048 | 0.86 |
| 45_K | 85_G | 1.047 | 0.85 |
| 26_V | 90_T | 1.047 | 0.85 |
| 57_Y | 77_F | 1.038 | 0.85 |
| 47_R | 73_W | 1.037 | 0.85 |
| 16_L | 19_G | 1.037 | 0.85 |
| 11_A | 14_L | 1.018 | 0.83 |
| 12_V | 15_M | 1.016 | 0.83 |
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 | 0.8142 | 99.9 | 0.308 | Contact Map |
| 2yh9A | 3 | 0.6018 | 99.9 | 0.319 | Contact Map |
| 2km7A | 1 | 0.8319 | 99.9 | 0.338 | Contact Map |
| 4dm5A | 4 | 0.6991 | 99.6 | 0.523 | Contact Map |
| 3gmvX | 1 | 0.6549 | 96.7 | 0.803 | Contact Map |
| 3n4iB | 1 | 0.6549 | 96.7 | 0.804 | Contact Map |
| 3d4eA | 1 | 0.9115 | 96.6 | 0.804 | Contact Map |
| 3gmxB | 2 | 0.646 | 96.6 | 0.806 | Contact Map |
| 3zbiC | 14 | 0.2478 | 88.4 | 0.859 | Contact Map |
| 2vpzA | 2 | 0.3982 | 69.1 | 0.884 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)