| DUF3339 |
| ID: | 1519419115 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 67 (67) | ||
| Sequences: | 248 (96.1) | ||
| Seq/Len: | 3.701 | ||
| Nf(neff/√len): | 11.7 |
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: 3.701).
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 |
| 36_N | 43_S | 3.055 | 1.00 |
| 8_L | 66_I | 2.228 | 1.00 |
| 57_I | 61_A | 1.959 | 1.00 |
| 5_G | 11_V | 1.854 | 1.00 |
| 28_K | 38_Q | 1.779 | 0.99 |
| 46_V | 64_V | 1.687 | 0.99 |
| 51_F | 56_A | 1.485 | 0.97 |
| 54_L | 58_L | 1.475 | 0.97 |
| 24_Q | 40_S | 1.466 | 0.97 |
| 40_S | 43_S | 1.465 | 0.97 |
| 6_P | 16_L | 1.415 | 0.96 |
| 7_V | 43_S | 1.412 | 0.96 |
| 1_M | 5_G | 1.336 | 0.93 |
| 58_L | 64_V | 1.302 | 0.92 |
| 5_G | 63_G | 1.294 | 0.92 |
| 30_R | 61_A | 1.282 | 0.91 |
| 31_G | 56_A | 1.270 | 0.91 |
| 5_G | 10_A | 1.268 | 0.91 |
| 36_N | 40_S | 1.251 | 0.90 |
| 5_G | 18_S | 1.219 | 0.89 |
| 1_M | 17_L | 1.218 | 0.88 |
| 49_L | 66_I | 1.183 | 0.86 |
| 8_L | 48_A | 1.181 | 0.86 |
| 51_F | 55_F | 1.143 | 0.84 |
| 41_G | 57_I | 1.139 | 0.84 |
| 7_V | 41_G | 1.137 | 0.83 |
| 22_L | 34_F | 1.085 | 0.79 |
| 4_W | 8_L | 1.079 | 0.79 |
| 49_L | 62_I | 1.073 | 0.78 |
| 10_A | 37_M | 1.067 | 0.78 |
| 29_S | 43_S | 1.067 | 0.78 |
| 58_L | 61_A | 1.058 | 0.77 |
| 39_T | 44_I | 1.050 | 0.76 |
| 32_V | 44_I | 1.048 | 0.76 |
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 | |
| 4nv4A | 2 | 0.2239 | 3.8 | 0.933 | Contact Map |
| 1kqfC | 1 | 0.8507 | 2.8 | 0.937 | Contact Map |
| 1b12A | 4 | 0.5672 | 2.7 | 0.938 | Contact Map |
| 2b2hA | 1 | 0.8955 | 2.3 | 0.94 | Contact Map |
| 4bqnA | 2 | 0.6418 | 2.1 | 0.941 | Contact Map |
| 1u7gA | 1 | 0.8955 | 1.9 | 0.943 | Contact Map |
| 3rceA | 1 | 0.4478 | 1.9 | 0.943 | Contact Map |
| 4d8pB | 2 | 0.0448 | 1.8 | 0.943 | Contact Map |
| 4httA | 2 | 1 | 1.7 | 0.944 | Contact Map |
| 4huqT | 1 | 0.2836 | 1.5 | 0.946 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)