| Fti4_1 |
| ID: | 1516554484 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 74 (57) | ||
| Sequences: | 304 (247.1) | ||
| Seq/Len: | 5.333 | ||
| Nf(neff/√len): | 32.7 |
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: 5.333).
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 |
| 52_R | 57_Q | 3.231 | 1.00 |
| 21_T | 24_E | 2.467 | 1.00 |
| 50_G | 54_L | 1.940 | 1.00 |
| 20_L | 24_E | 1.845 | 1.00 |
| 42_L | 47_I | 1.779 | 1.00 |
| 43_N | 46_D | 1.533 | 0.99 |
| 32_I | 42_L | 1.515 | 0.99 |
| 32_I | 47_I | 1.504 | 0.99 |
| 32_I | 35_Y | 1.433 | 0.98 |
| 39_N | 42_L | 1.422 | 0.98 |
| 28_I | 54_L | 1.386 | 0.98 |
| 53_I | 68_K | 1.339 | 0.97 |
| 45_D | 56_G | 1.231 | 0.94 |
| 35_Y | 40_M | 1.220 | 0.94 |
| 49_A | 66_K | 1.206 | 0.93 |
| 35_Y | 43_N | 1.172 | 0.92 |
| 62_E | 65_L | 1.144 | 0.91 |
| 34_N | 38_E | 1.127 | 0.90 |
| 33_G | 42_L | 1.112 | 0.89 |
| 48_L | 52_R | 1.078 | 0.87 |
| 40_M | 46_D | 1.077 | 0.87 |
| 61_Q | 65_L | 1.069 | 0.86 |
| 49_A | 58_A | 1.043 | 0.84 |
| 53_I | 58_A | 1.026 | 0.83 |
| 30_S | 34_N | 1.021 | 0.83 |
| 27_S | 65_L | 1.013 | 0.82 |
| 25_Y | 32_I | 1.013 | 0.82 |
| 49_A | 63_E | 1.002 | 0.81 |
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 | |
| 3shgB | 1 | 0.8108 | 98.1 | 0.596 | Contact Map |
| 4ociA | 1 | 0.7973 | 36.5 | 0.85 | Contact Map |
| 3cucA | 2 | 0.9459 | 32.9 | 0.854 | Contact Map |
| 4mzjA | 1 | 0.9189 | 30.2 | 0.857 | Contact Map |
| 4m70R | 1 | 0.0811 | 23 | 0.865 | Contact Map |
| 2h2kA | 2 | 0.973 | 20.9 | 0.867 | Contact Map |
| 1ggwA | 1 | 0.8784 | 18.5 | 0.87 | Contact Map |
| 3j04B | 2 | 0.9054 | 17.5 | 0.872 | Contact Map |
| 2kz2A | 1 | 0.9054 | 17.5 | 0.872 | Contact Map |
| 3a1kA | 1 | 0.7162 | 17.1 | 0.872 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)