| d4furb_ |
| ID: | 1450281973 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 98 (98) | ||
| Sequences: | 824 (258.9) | ||
| Seq/Len: | 8.408 | ||
| Nf(neff/√len): | 26.2 |
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: 8.408).
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 |
| 22_K | 66_D | 4.709 | 1.00 |
| 24_K | 47_E | 3.607 | 1.00 |
| 45_A | 82_A | 3.078 | 1.00 |
| 12_H | 16_D | 2.298 | 1.00 |
| 16_D | 20_K | 2.274 | 1.00 |
| 59_R | 98_T | 2.195 | 1.00 |
| 44_G | 54_V | 2.062 | 1.00 |
| 37_L | 93_L | 2.061 | 1.00 |
| 41_V | 93_L | 2.045 | 1.00 |
| 40_Y | 57_G | 1.981 | 1.00 |
| 15_S | 39_A | 1.830 | 1.00 |
| 12_H | 20_K | 1.822 | 1.00 |
| 51_V | 55_M | 1.775 | 1.00 |
| 36_V | 61_V | 1.729 | 1.00 |
| 4_R | 8_K | 1.700 | 1.00 |
| 13_M | 16_D | 1.676 | 1.00 |
| 16_D | 19_L | 1.585 | 1.00 |
| 40_Y | 61_V | 1.581 | 1.00 |
| 64_A | 73_D | 1.555 | 1.00 |
| 64_A | 72_P | 1.533 | 1.00 |
| 30_H | 34_V | 1.529 | 1.00 |
| 11_I | 38_S | 1.505 | 1.00 |
| 11_I | 15_S | 1.491 | 1.00 |
| 26_L | 47_E | 1.436 | 0.99 |
| 19_L | 40_Y | 1.391 | 0.99 |
| 34_V | 75_L | 1.338 | 0.99 |
| 51_V | 94_H | 1.320 | 0.99 |
| 13_M | 19_L | 1.306 | 0.99 |
| 55_M | 58_A | 1.301 | 0.98 |
| 14_L | 89_R | 1.277 | 0.98 |
| 22_K | 36_V | 1.193 | 0.97 |
| 57_G | 60_S | 1.186 | 0.97 |
| 30_H | 74_L | 1.185 | 0.97 |
| 6_F | 10_V | 1.172 | 0.96 |
| 19_L | 39_A | 1.162 | 0.96 |
| 79_Q | 92_S | 1.161 | 0.96 |
| 21_R | 29_N | 1.094 | 0.94 |
| 70_G | 73_D | 1.086 | 0.94 |
| 15_S | 36_V | 1.082 | 0.94 |
| 57_G | 61_V | 1.052 | 0.93 |
| 66_D | 89_R | 1.019 | 0.91 |
| 17_V | 39_A | 1.013 | 0.91 |
| 56_D | 60_S | 1.008 | 0.90 |
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 | |
| 2fvhA | 3 | 1 | 100 | -0.021 | Contact Map |
| 4gy7A | 1 | 0.9898 | 100 | -0.019 | Contact Map |
| 1e9yA | 1 | 1 | 100 | -0.012 | Contact Map |
| 3qgaA | 6 | 1 | 100 | -0.012 | Contact Map |
| 4furA | 6 | 1 | 100 | -0.011 | Contact Map |
| 4ac7A | 1 | 1 | 100 | -0.011 | Contact Map |
| 1szqA | 2 | 0.9388 | 25.7 | 0.931 | Contact Map |
| 4d2uA | 6 | 0.8571 | 15.1 | 0.938 | Contact Map |
| 1tlqA | 1 | 0.6939 | 12.7 | 0.94 | Contact Map |
| 1qvrA | 3 | 0.8571 | 11.1 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)