| AraC Arm only |
| ID: | 1495809320 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 38 (37) | ||
| Sequences: | 85 (36.2) | ||
| Seq/Len: | 2.297 | ||
| Nf(neff/√len): | 6.0 |
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: 2.297).
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 |
| 7_D | 10_L | 2.227 | 1.00 |
| 18_H | 21_A | 2.166 | 1.00 |
| 7_D | 18_H | 2.000 | 0.99 |
| 8_P | 13_Y | 1.863 | 0.99 |
| 32_L | 36_I | 1.787 | 0.98 |
| 11_P | 34_F | 1.685 | 0.97 |
| 23_L | 37_D | 1.399 | 0.89 |
| 30_G | 37_D | 1.329 | 0.86 |
| 10_L | 13_Y | 1.312 | 0.85 |
| 25_P | 30_G | 1.310 | 0.85 |
| 4_T | 28_A | 1.276 | 0.82 |
| 12_G | 34_F | 1.216 | 0.78 |
| 20_V | 32_L | 1.196 | 0.76 |
| 17_A | 21_A | 1.194 | 0.76 |
| 12_G | 19_L | 1.135 | 0.71 |
| 9_L | 26_I | 1.090 | 0.66 |
| 26_I | 36_I | 1.007 | 0.57 |
| 10_L | 23_L | 1.000 | 0.56 |
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 | 0.8421 | 95.4 | 0.659 | Contact Map |
| 1m9sA | 1 | 0 | 3.7 | 0.885 | Contact Map |
| 1ofwA | 2 | 0.4737 | 3.6 | 0.885 | Contact Map |
| 1ut7A | 2 | 1 | 3.5 | 0.886 | Contact Map |
| 1m1hA | 1 | 1 | 3.5 | 0.886 | Contact Map |
| 4bmoA | 1 | 0.6842 | 3.1 | 0.889 | Contact Map |
| 3fluA | 4 | 0.7368 | 2.7 | 0.893 | Contact Map |
| 3cprA | 2 | 0.9737 | 2.5 | 0.894 | Contact Map |
| 3memA | 1 | 0.8684 | 2.5 | 0.895 | Contact Map |
| 3op6A | 2 | 0.8684 | 2.5 | 0.895 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)