| 806_9 |
| ID: | 1433407225 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 34 (34) | ||
| Sequences: | 54 (26.6) | ||
| Seq/Len: | 1.588 | ||
| Nf(neff/√len): | 4.6 |
HHblits Results: (2013_03)
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: 1.588).
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 |
| 30_N | 34_F | 2.223 | 0.99 |
| 7_V | 19_L | 1.842 | 0.97 |
| 6_T | 19_L | 1.822 | 0.96 |
| 13_Q | 33_I | 1.594 | 0.91 |
| 15_G | 20_Q | 1.511 | 0.88 |
| 25_F | 28_P | 1.508 | 0.88 |
| 25_F | 31_D | 1.475 | 0.86 |
| 27_A | 31_D | 1.471 | 0.86 |
| 28_P | 31_D | 1.355 | 0.79 |
| 14_Y | 19_L | 1.298 | 0.75 |
| 2_L | 25_F | 1.269 | 0.72 |
| 13_Q | 18_V | 1.266 | 0.72 |
| 14_Y | 33_I | 1.121 | 0.58 |
| 8_S | 26_G | 1.111 | 0.57 |
| 10_F | 26_G | 1.094 | 0.55 |
| 3_R | 11_L | 1.069 | 0.53 |
| 5_Y | 10_F | 1.054 | 0.51 |
| 7_V | 11_L | 1.034 | 0.49 |
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 | |
| 3gvoA | 1 | 1 | 97.2 | 0.61 | Contact Map |
| 3k62A | 1 | 1 | 96.9 | 0.63 | Contact Map |
| 3k49A | 3 | 1 | 96.9 | 0.63 | Contact Map |
| 3v71A | 1 | 1 | 96.4 | 0.652 | Contact Map |
| 4wzrA | 2 | 1 | 95.2 | 0.683 | Contact Map |
| 3bwtA | 1 | 1 | 85.7 | 0.752 | Contact Map |
| 3ismC | 1 | 0.9706 | 10.1 | 0.867 | Contact Map |
| 3agdA | 2 | 1 | 5.5 | 0.882 | Contact Map |
| 4x01A | 8 | 0.9118 | 4.7 | 0.885 | Contact Map |
| 2wnsA | 2 | 0.6471 | 4.5 | 0.887 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)