| 1wvn_A |
| ID: | 1438079474 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 74 (72) | ||
| Sequences: | 112 (68.8) | ||
| Seq/Len: | 1.556 | ||
| Nf(neff/√len): | 8.1 |
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: 1.556).
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 |
| 57_G | 65_A | 1.708 | 0.94 |
| 23_R | 32_R | 1.700 | 0.94 |
| 45_V | 50_G | 1.669 | 0.93 |
| 8_H | 11_T | 1.577 | 0.90 |
| 36_G | 67_Y | 1.545 | 0.89 |
| 33_Q | 36_G | 1.423 | 0.83 |
| 12_I | 22_G | 1.385 | 0.80 |
| 21_I | 57_G | 1.368 | 0.79 |
| 56_T | 73_L | 1.364 | 0.79 |
| 7_T | 48_S | 1.347 | 0.78 |
| 35_S | 51_R | 1.344 | 0.78 |
| 22_G | 32_R | 1.341 | 0.77 |
| 11_T | 50_G | 1.319 | 0.76 |
| 21_I | 32_R | 1.303 | 0.74 |
| 43_N | 64_L | 1.277 | 0.72 |
| 19_C | 27_N | 1.264 | 0.71 |
| 19_C | 40_K | 1.251 | 0.70 |
| 21_I | 65_A | 1.237 | 0.69 |
| 28_I | 35_S | 1.214 | 0.67 |
| 37_A | 41_I | 1.211 | 0.66 |
| 8_H | 46_E | 1.195 | 0.65 |
| 16_L | 66_Q | 1.193 | 0.65 |
| 63_S | 69_I | 1.180 | 0.63 |
| 9_E | 70_N | 1.169 | 0.62 |
| 43_N | 46_E | 1.162 | 0.62 |
| 18_G | 28_I | 1.159 | 0.61 |
| 22_G | 51_R | 1.157 | 0.61 |
| 18_G | 25_G | 1.135 | 0.59 |
| 32_R | 35_S | 1.114 | 0.57 |
| 10_L | 70_N | 1.112 | 0.57 |
| 58_S | 67_Y | 1.101 | 0.56 |
| 3_G | 26_A | 1.091 | 0.55 |
| 16_L | 62_I | 1.068 | 0.52 |
| 25_G | 32_R | 1.063 | 0.52 |
| 25_G | 28_I | 1.057 | 0.51 |
| 29_N | 40_K | 1.055 | 0.51 |
| 13_P | 16_L | 1.035 | 0.49 |
| 10_L | 63_S | 1.017 | 0.47 |
| 23_R | 48_S | 1.015 | 0.47 |
| 10_L | 17_I | 1.014 | 0.47 |
| 6_T | 15_N | 1.014 | 0.47 |
| 28_I | 32_R | 1.014 | 0.47 |
| 38_Q | 50_G | 1.014 | 0.47 |
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 | |
| 1wvnA | 1 | 1 | 99.6 | 0.498 | Contact Map |
| 3v69A | 2 | 0.9865 | 99.6 | 0.501 | Contact Map |
| 3n89A | 2 | 0.9324 | 99.6 | 0.506 | Contact Map |
| 1j5kA | 1 | 0.9865 | 99.5 | 0.517 | Contact Map |
| 2p2rA | 1 | 0.9595 | 99.5 | 0.517 | Contact Map |
| 1zzkA | 1 | 0.9865 | 99.5 | 0.518 | Contact Map |
| 4lijA | 3 | 1 | 99.5 | 0.522 | Contact Map |
| 1x4nA | 1 | 1 | 99.5 | 0.523 | Contact Map |
| 1we8A | 1 | 0.9865 | 99.4 | 0.54 | Contact Map |
| 1dtjA | 4 | 0.9595 | 99.4 | 0.54 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)