| n2a_e04_8_50 |
| ID: | 1510234914 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 111 (71) | ||
| Sequences: | 100 (67.9) | ||
| Seq/Len: | 1.408 | ||
| Nf(neff/√len): | 8.1 |
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: 1.408).
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 |
| 36_I | 57_I | 2.047 | 0.98 |
| 45_P | 65_Q | 1.982 | 0.98 |
| 47_E | 54_M | 1.982 | 0.98 |
| 43_V | 51_Y | 1.850 | 0.96 |
| 13_D | 19_K | 1.841 | 0.96 |
| 20_K | 72_Q | 1.830 | 0.96 |
| 36_I | 70_L | 1.670 | 0.92 |
| 38_E | 58_T | 1.614 | 0.90 |
| 47_E | 52_A | 1.569 | 0.88 |
| 37_M | 63_L | 1.560 | 0.88 |
| 31_E | 34_I | 1.499 | 0.85 |
| 34_I | 50_K | 1.450 | 0.82 |
| 46_K | 60_F | 1.422 | 0.80 |
| 40_L | 61_R | 1.419 | 0.80 |
| 34_I | 48_Y | 1.358 | 0.76 |
| 14_L | 18_L | 1.317 | 0.73 |
| 27_G | 30_E | 1.279 | 0.70 |
| 66_A | 69_L | 1.224 | 0.65 |
| 45_P | 52_A | 1.186 | 0.61 |
| 48_Y | 51_Y | 1.153 | 0.58 |
| 33_E | 54_M | 1.131 | 0.56 |
| 74_Q | 77_E | 1.129 | 0.55 |
| 55_Y | 62_G | 1.119 | 0.54 |
| 16_A | 41_K | 1.100 | 0.52 |
| 36_I | 63_L | 1.097 | 0.52 |
| 16_A | 52_A | 1.095 | 0.52 |
| 43_V | 67_F | 1.093 | 0.52 |
| 13_D | 18_L | 1.088 | 0.51 |
| 51_Y | 63_L | 1.086 | 0.51 |
| 23_I | 27_G | 1.064 | 0.49 |
| 24_L | 29_G | 1.061 | 0.49 |
| 56_G | 62_G | 1.059 | 0.48 |
| 54_M | 58_T | 1.049 | 0.47 |
| 17_M | 28_A | 1.039 | 0.46 |
| 22_P | 25_K | 1.039 | 0.46 |
| 16_A | 47_E | 1.024 | 0.45 |
| 36_I | 39_L | 1.022 | 0.45 |
| 15_R | 57_I | 1.020 | 0.44 |
| 21_T | 25_K | 1.013 | 0.44 |
| 14_L | 19_K | 1.007 | 0.43 |
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 | |
| 2lhuA | 1 | 0.3153 | 99.9 | 0.352 | Contact Map |
| 3hv0A | 2 | 0.4775 | 10.8 | 0.924 | Contact Map |
| 4iz7B | 1 | 0.4865 | 10 | 0.925 | Contact Map |
| 2ip1A | 1 | 0.4955 | 6.9 | 0.93 | Contact Map |
| 1r6tA | 2 | 0.8198 | 6.8 | 0.931 | Contact Map |
| 3a04A | 1 | 0.5766 | 6.5 | 0.931 | Contact Map |
| 4rb5O | 1 | 0.4234 | 5.9 | 0.932 | Contact Map |
| 4a5uB | 1 | 0.3514 | 5.7 | 0.933 | Contact Map |
| 1q2zA | 1 | 0.8829 | 5.3 | 0.934 | Contact Map |
| 4j76A | 2 | 0.5135 | 4.9 | 0.935 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)