| AraC 1-75 |
| ID: | 1496876299 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 75 (72) | ||
| Sequences: | 122 (55.2) | ||
| Seq/Len: | 1.694 | ||
| Nf(neff/√len): | 6.5 |
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: 1.694).
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 |
| 42_M | 74_F | 2.297 | 1.00 |
| 7_D | 18_H | 2.098 | 0.99 |
| 7_D | 10_L | 1.930 | 0.98 |
| 18_H | 21_A | 1.744 | 0.96 |
| 23_L | 37_D | 1.695 | 0.95 |
| 64_F | 72_L | 1.572 | 0.91 |
| 27_E | 49_L | 1.548 | 0.90 |
| 6_N | 47_L | 1.500 | 0.88 |
| 54_Q | 67_R | 1.432 | 0.85 |
| 8_P | 13_Y | 1.430 | 0.85 |
| 30_G | 51_I | 1.391 | 0.83 |
| 60_Q | 71_I | 1.381 | 0.82 |
| 48_N | 70_D | 1.335 | 0.79 |
| 26_I | 36_I | 1.334 | 0.79 |
| 14_S | 35_F | 1.308 | 0.77 |
| 28_A | 62_R | 1.291 | 0.76 |
| 5_Q | 68_P | 1.279 | 0.75 |
| 21_A | 58_K | 1.261 | 0.73 |
| 30_G | 57_V | 1.260 | 0.73 |
| 18_H | 66_C | 1.246 | 0.72 |
| 21_A | 57_V | 1.237 | 0.71 |
| 57_V | 64_F | 1.235 | 0.71 |
| 11_P | 34_F | 1.207 | 0.69 |
| 10_L | 13_Y | 1.194 | 0.67 |
| 16_N | 35_F | 1.155 | 0.64 |
| 37_D | 68_P | 1.152 | 0.63 |
| 25_P | 30_G | 1.115 | 0.60 |
| 10_L | 66_C | 1.089 | 0.57 |
| 49_L | 62_R | 1.087 | 0.57 |
| 10_L | 45_Y | 1.081 | 0.56 |
| 14_S | 67_R | 1.065 | 0.54 |
| 8_P | 36_I | 1.063 | 0.54 |
| 7_D | 45_Y | 1.054 | 0.53 |
| 25_P | 70_D | 1.052 | 0.53 |
| 4_A | 28_A | 1.046 | 0.52 |
| 39_P | 46_I | 1.044 | 0.52 |
| 22_G | 50_T | 1.035 | 0.51 |
| 4_A | 40_L | 1.013 | 0.49 |
| 4_A | 67_R | 1.004 | 0.48 |
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 | |
| 2arcA | 2 | 0.92 | 98.9 | 0.683 | Contact Map |
| 4mv2A | 2 | 0.9333 | 88 | 0.864 | Contact Map |
| 3gbgA | 1 | 0.76 | 80.1 | 0.877 | Contact Map |
| 2qnkA | 1 | 0.9733 | 73.9 | 0.883 | Contact Map |
| 4rd7A | 1 | 0.9333 | 71 | 0.886 | Contact Map |
| 2f4pA | 4 | 0.92 | 68.5 | 0.888 | Contact Map |
| 1v70A | 1 | 0.88 | 68.2 | 0.888 | Contact Map |
| 2ozjA | 2 | 0.88 | 67.9 | 0.888 | Contact Map |
| 3bu7A | 2 | 0.92 | 67.4 | 0.889 | Contact Map |
| 1sefA | 1 | 0.9467 | 67.1 | 0.889 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)