| 1234 |
| ID: | 1463584858 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 154 (147) | ||
| Sequences: | 2906 (2168.5) | ||
| Seq/Len: | 19.769 | ||
| Nf(neff/√len): | 178.9 |
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: 19.769).
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 |
| 138_S | 142_E | 3.141 | 1.00 |
| 50_V | 67_F | 3.024 | 1.00 |
| 53_V | 63_H | 2.878 | 1.00 |
| 141_L | 144_Y | 2.629 | 1.00 |
| 43_E | 71_E | 2.622 | 1.00 |
| 67_F | 71_E | 2.620 | 1.00 |
| 40_L | 139_E | 2.554 | 1.00 |
| 54_E | 62_T | 2.436 | 1.00 |
| 141_L | 146_L | 2.315 | 1.00 |
| 78_H | 136_E | 2.315 | 1.00 |
| 37_G | 131_R | 2.218 | 1.00 |
| 144_Y | 147_G | 1.987 | 1.00 |
| 89_M | 92_G | 1.881 | 1.00 |
| 77_Y | 81_D | 1.837 | 1.00 |
| 14_P | 17_R | 1.819 | 1.00 |
| 47_E | 64_K | 1.800 | 1.00 |
| 42_K | 46_E | 1.795 | 1.00 |
| 46_E | 67_F | 1.750 | 1.00 |
| 27_E | 124_M | 1.626 | 1.00 |
| 65_A | 68_W | 1.625 | 1.00 |
| 82_C | 133_L | 1.584 | 1.00 |
| 85_T | 129_E | 1.579 | 1.00 |
| 71_E | 143_R | 1.558 | 1.00 |
| 46_E | 70_D | 1.554 | 1.00 |
| 55_H | 69_M | 1.491 | 1.00 |
| 142_E | 146_L | 1.440 | 1.00 |
| 37_G | 134_V | 1.429 | 1.00 |
| 3_A | 6_S | 1.426 | 1.00 |
| 40_L | 134_V | 1.411 | 1.00 |
| 91_S | 95_D | 1.386 | 0.99 |
| 47_E | 143_R | 1.380 | 0.99 |
| 140_R | 144_Y | 1.338 | 0.99 |
| 54_E | 63_H | 1.327 | 0.99 |
| 141_L | 147_G | 1.299 | 0.99 |
| 27_E | 31_P | 1.291 | 0.99 |
| 75_L | 140_R | 1.289 | 0.99 |
| 39_E | 42_K | 1.265 | 0.99 |
| 73_R | 80_E | 1.243 | 0.98 |
| 9_L | 13_G | 1.243 | 0.98 |
| 30_L | 127_I | 1.242 | 0.98 |
| 46_E | 71_E | 1.233 | 0.98 |
| 106_V | 109_A | 1.230 | 0.98 |
| 130_L | 134_V | 1.229 | 0.98 |
| 68_W | 144_Y | 1.202 | 0.98 |
| 54_E | 58_V | 1.175 | 0.98 |
| 47_E | 67_F | 1.173 | 0.98 |
| 105_K | 108_R | 1.159 | 0.97 |
| 36_E | 132_A | 1.149 | 0.97 |
| 124_M | 128_A | 1.144 | 0.97 |
| 140_R | 146_L | 1.135 | 0.97 |
| 139_E | 143_R | 1.126 | 0.97 |
| 37_G | 123_R | 1.108 | 0.96 |
| 68_W | 72_V | 1.073 | 0.95 |
| 12_M | 15_L | 1.069 | 0.95 |
| 143_R | 146_L | 1.062 | 0.95 |
| 54_E | 65_A | 1.060 | 0.95 |
| 74_D | 77_Y | 1.059 | 0.95 |
| 51_S | 55_H | 1.054 | 0.95 |
| 18_K | 22_L | 1.047 | 0.94 |
| 145_Q | 148_D | 1.030 | 0.94 |
| 9_L | 14_P | 1.026 | 0.94 |
| 88_S | 91_S | 1.026 | 0.94 |
| 41_L | 79_I | 1.012 | 0.93 |
| 129_E | 132_A | 1.008 | 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 | |
| 3qflA | 1 | 0.6948 | 99.8 | 0.248 | Contact Map |
| 4m70A | 5 | 0.7403 | 68.6 | 0.835 | Contact Map |
| 2a5yB | 2 | 0.6883 | 36.6 | 0.865 | Contact Map |
| 4btfA | 1 | 0.6364 | 14.8 | 0.887 | Contact Map |
| 1vcsA | 1 | 0.6494 | 12.1 | 0.892 | Contact Map |
| 3terA | 2 | 0.6753 | 11.4 | 0.893 | Contact Map |
| 1vt4I | 8 | 0.6299 | 6.3 | 0.905 | Contact Map |
| 4xa3A | 2 | 0 | 5.7 | 0.907 | Contact Map |
| 1sumB | 1 | 0.7143 | 5.4 | 0.908 | Contact Map |
| 3a7pA | 2 | 0.4351 | 4.9 | 0.91 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)