| 2mhr |
| ID: | 1486855234 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 118 (114) | ||
| Sequences: | 1741 (1460.4) | ||
| Seq/Len: | 15.272 | ||
| Nf(neff/√len): | 136.8 |
HHblits Results: (2016_02)
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: 15.272).
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 |
| 24_E | 57_H | 4.831 | 1.00 |
| 12_E | 15_R | 3.423 | 1.00 |
| 68_S | 117_K | 3.272 | 1.00 |
| 63_D | 70_V | 2.749 | 1.00 |
| 34_D | 46_T | 2.306 | 1.00 |
| 76_M | 110_T | 2.258 | 1.00 |
| 112_F | 115_K | 1.989 | 1.00 |
| 27_K | 30_K | 1.970 | 1.00 |
| 62_M | 70_V | 1.908 | 1.00 |
| 31_G | 46_T | 1.869 | 1.00 |
| 62_M | 114_Y | 1.842 | 1.00 |
| 11_D | 14_F | 1.758 | 1.00 |
| 28_I | 103_L | 1.753 | 1.00 |
| 53_N | 57_H | 1.703 | 1.00 |
| 74_K | 78_K | 1.681 | 1.00 |
| 63_D | 74_K | 1.653 | 1.00 |
| 52_T | 81_L | 1.650 | 1.00 |
| 25_H | 54_H | 1.643 | 1.00 |
| 19_E | 23_E | 1.617 | 1.00 |
| 10_W | 15_R | 1.591 | 1.00 |
| 16_V | 115_K | 1.565 | 1.00 |
| 70_V | 78_K | 1.558 | 1.00 |
| 48_V | 88_S | 1.550 | 1.00 |
| 60_A | 64_A | 1.548 | 1.00 |
| 7_P | 36_I | 1.499 | 1.00 |
| 70_V | 74_K | 1.497 | 1.00 |
| 20_Q | 57_H | 1.467 | 1.00 |
| 27_K | 46_T | 1.454 | 1.00 |
| 26_K | 30_K | 1.419 | 1.00 |
| 69_E | 113_K | 1.357 | 0.99 |
| 69_E | 72_P | 1.267 | 0.99 |
| 10_W | 26_K | 1.261 | 0.99 |
| 75_K | 79_D | 1.250 | 0.99 |
| 77_H | 111_D | 1.242 | 0.98 |
| 83_K | 86_G | 1.235 | 0.98 |
| 52_T | 85_G | 1.219 | 0.98 |
| 23_E | 26_K | 1.219 | 0.98 |
| 61_M | 65_A | 1.204 | 0.98 |
| 30_K | 34_D | 1.200 | 0.98 |
| 48_V | 85_G | 1.186 | 0.98 |
| 25_H | 58_E | 1.182 | 0.98 |
| 56_T | 60_A | 1.179 | 0.98 |
| 65_A | 117_K | 1.160 | 0.97 |
| 110_T | 113_K | 1.157 | 0.97 |
| 106_H | 111_D | 1.100 | 0.96 |
| 16_V | 21_L | 1.099 | 0.96 |
| 82_E | 86_G | 1.080 | 0.95 |
| 45_A | 88_S | 1.062 | 0.95 |
| 59_E | 74_K | 1.056 | 0.95 |
| 21_L | 61_M | 1.055 | 0.95 |
| 41_A | 91_V | 1.037 | 0.94 |
| 14_F | 108_K | 1.014 | 0.93 |
| 51_T | 80_F | 1.010 | 0.93 |
| 78_K | 81_L | 1.000 | 0.92 |
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 | |
| 2mhrA | 1 | 1 | 100 | 0.014 | Contact Map |
| 2hmqA | 4 | 0.9576 | 100 | 0.034 | Contact Map |
| 3agtA | 2 | 0.9576 | 100 | 0.09 | Contact Map |
| 4xpxA | 1 | 0 | 99.9 | 0.1 | Contact Map |
| 2p0nA | 2 | 0.8644 | 86 | 0.833 | Contact Map |
| 3caxA | 1 | 0.9068 | 83.5 | 0.838 | Contact Map |
| 3cljA | 1 | 0.3644 | 6.2 | 0.918 | Contact Map |
| 3k1dA | 1 | 0.8983 | 3.8 | 0.926 | Contact Map |
| 3b5mA | 4 | 0.4746 | 3.3 | 0.928 | Contact Map |
| 3tj1A | 2 | 0.9915 | 3.3 | 0.929 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)