| VW |
| ID: | 1487583276 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 66 (66) | ||
| Sequences: | 232 (117.4) | ||
| Seq/Len: | 3.515 | ||
| Nf(neff/√len): | 14.5 |
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: 3.515).
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 |
| 45_P | 65_W | 1.974 | 1.00 |
| 2_A | 29_D | 1.912 | 1.00 |
| 24_Q | 44_L | 1.898 | 1.00 |
| 60_K | 64_E | 1.644 | 0.98 |
| 22_K | 26_T | 1.560 | 0.98 |
| 11_Y | 17_F | 1.523 | 0.97 |
| 8_G | 18_Q | 1.453 | 0.96 |
| 4_C | 8_G | 1.437 | 0.96 |
| 26_T | 33_G | 1.437 | 0.96 |
| 30_G | 34_C | 1.400 | 0.95 |
| 4_C | 11_Y | 1.397 | 0.95 |
| 11_Y | 14_G | 1.393 | 0.95 |
| 13_S | 31_A | 1.363 | 0.94 |
| 44_L | 48_D | 1.316 | 0.92 |
| 9_T | 12_R | 1.296 | 0.91 |
| 20_S | 42_V | 1.288 | 0.91 |
| 4_C | 14_G | 1.287 | 0.91 |
| 3_P | 15_E | 1.284 | 0.91 |
| 39_S | 46_S | 1.259 | 0.90 |
| 14_G | 17_F | 1.255 | 0.90 |
| 21_C | 38_C | 1.250 | 0.89 |
| 1_G | 13_S | 1.240 | 0.89 |
| 47_P | 50_P | 1.186 | 0.86 |
| 27_C | 30_G | 1.183 | 0.85 |
| 35_M | 54_R | 1.180 | 0.85 |
| 34_C | 49_C | 1.108 | 0.80 |
| 50_P | 58_P | 1.065 | 0.76 |
| 62_C | 65_W | 1.032 | 0.73 |
| 25_C | 30_G | 1.030 | 0.73 |
| 41_D | 54_R | 1.030 | 0.73 |
| 8_G | 17_F | 1.024 | 0.72 |
| 1_G | 33_G | 1.005 | 0.70 |
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 | |
| 1u5mA | 1 | 0.9091 | 98.4 | 0.602 | Contact Map |
| 3bk3C | 2 | 0.8939 | 96.6 | 0.718 | Contact Map |
| 2mhpA | 1 | 0.5909 | 95.6 | 0.743 | Contact Map |
| 3tjqA | 1 | 0.5909 | 31.3 | 0.868 | Contact Map |
| 2cg7A | 1 | 0.5606 | 28.4 | 0.871 | Contact Map |
| 1wo9A | 1 | 0.5152 | 27.1 | 0.872 | Contact Map |
| 2xttA | 1 | 0.5 | 23.5 | 0.876 | Contact Map |
| 1gl0I | 1 | 0.4697 | 11.1 | 0.893 | Contact Map |
| 1o9aA | 1 | 0.5909 | 9.8 | 0.896 | Contact Map |
| 2rl0A | 6 | 0.5455 | 5.9 | 0.906 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)