| whatisthis |
| ID: | 1433388210 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 35 (35) | ||
| Sequences: | 95 (74.6) | ||
| Seq/Len: | 2.714 | ||
| Nf(neff/√len): | 12.6 |
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: 2.714).
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_V | 33_S | 1.632 | 0.97 |
| 12_D | 16_N | 1.610 | 0.97 |
| 26_G | 32_D | 1.507 | 0.95 |
| 12_D | 18_V | 1.503 | 0.95 |
| 26_G | 31_A | 1.469 | 0.94 |
| 4_Y | 28_N | 1.426 | 0.93 |
| 10_V | 30_F | 1.393 | 0.92 |
| 5_N | 31_A | 1.278 | 0.86 |
| 13_P | 21_Y | 1.273 | 0.86 |
| 27_D | 35_I | 1.262 | 0.85 |
| 26_G | 35_I | 1.229 | 0.83 |
| 1_E | 11_Q | 1.170 | 0.79 |
| 13_P | 19_V | 1.130 | 0.75 |
| 1_E | 28_N | 1.120 | 0.74 |
| 9_L | 19_V | 1.085 | 0.71 |
| 21_Y | 24_D | 1.047 | 0.67 |
| 6_A | 10_V | 1.043 | 0.66 |
| 27_D | 32_D | 1.039 | 0.66 |
| 12_D | 17_Y | 1.038 | 0.66 |
| 13_P | 22_V | 1.010 | 0.63 |
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 | 98.3 | 0.351 | Contact Map |
| 3k62A | 1 | 1 | 98.1 | 0.379 | Contact Map |
| 3v71A | 1 | 1 | 98.1 | 0.388 | Contact Map |
| 4wzrA | 2 | 1 | 97.8 | 0.424 | Contact Map |
| 3k49A | 3 | 1 | 97.7 | 0.439 | Contact Map |
| 3bwtA | 1 | 1 | 96.5 | 0.533 | Contact Map |
| 3mtvA | 1 | 0.9714 | 18.6 | 0.801 | Contact Map |
| 1iimA | 2 | 0.6286 | 6.5 | 0.838 | Contact Map |
| 1lvwA | 4 | 0.8 | 6.2 | 0.84 | Contact Map |
| 4eyyR | 1 | 0.2 | 5.7 | 0.842 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)