| d2wnra2 |
| ID: | 1448598691 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 82 (82) | ||
| Sequences: | 2970 (1862.8) | ||
| Seq/Len: | 36.220 | ||
| Nf(neff/√len): | 205.7 |
HHblits Results: (2015_06)
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: 36.220).
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 |
| 20_L | 70_K | 3.026 | 1.00 |
| 4_R | 40_E | 2.676 | 1.00 |
| 36_I | 67_A | 2.676 | 1.00 |
| 57_R | 68_V | 2.586 | 1.00 |
| 12_A | 22_P | 2.533 | 1.00 |
| 57_R | 61_L | 2.518 | 1.00 |
| 4_R | 41_E | 2.371 | 1.00 |
| 5_K | 75_I | 2.248 | 1.00 |
| 7_L | 71_V | 2.189 | 1.00 |
| 76_E | 80_K | 1.925 | 1.00 |
| 77_Y | 80_K | 1.899 | 1.00 |
| 69_E | 73_Q | 1.850 | 1.00 |
| 5_K | 79_D | 1.761 | 1.00 |
| 13_K | 59_D | 1.670 | 1.00 |
| 56_T | 59_D | 1.558 | 1.00 |
| 14_I | 19_V | 1.452 | 1.00 |
| 57_R | 65_S | 1.422 | 1.00 |
| 71_V | 75_I | 1.393 | 0.99 |
| 12_A | 30_L | 1.386 | 0.99 |
| 38_V | 71_V | 1.368 | 0.99 |
| 19_V | 23_S | 1.305 | 0.99 |
| 4_R | 39_T | 1.287 | 0.99 |
| 73_Q | 76_E | 1.257 | 0.99 |
| 18_I | 66_I | 1.243 | 0.98 |
| 14_I | 29_I | 1.233 | 0.98 |
| 73_Q | 77_Y | 1.214 | 0.98 |
| 39_T | 43_S | 1.207 | 0.98 |
| 8_M | 37_G | 1.188 | 0.98 |
| 11_F | 34_I | 1.184 | 0.98 |
| 11_F | 36_I | 1.166 | 0.97 |
| 61_L | 65_S | 1.156 | 0.97 |
| 7_L | 74_L | 1.149 | 0.97 |
| 72_P | 76_E | 1.131 | 0.97 |
| 11_F | 67_A | 1.115 | 0.96 |
| 33_R | 48_Q | 1.105 | 0.96 |
| 8_M | 35_S | 1.101 | 0.96 |
| 36_I | 64_V | 1.054 | 0.95 |
| 65_S | 68_V | 1.047 | 0.94 |
| 39_T | 45_C | 1.037 | 0.94 |
| 18_I | 59_D | 1.026 | 0.94 |
| 5_K | 40_E | 1.010 | 0.93 |
| 68_V | 72_P | 1.009 | 0.93 |
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 | |
| 2po1B | 1 | 1 | 99.5 | 0.151 | Contact Map |
| 2je6A | 1 | 1 | 99.5 | 0.152 | Contact Map |
| 2wnrA | 3 | 1 | 99.5 | 0.159 | Contact Map |
| 2nn6E | 1 | 1 | 99.5 | 0.16 | Contact Map |
| 1r6lA | 1 | 1 | 99.4 | 0.173 | Contact Map |
| 1udnA | 1 | 1 | 99.4 | 0.173 | Contact Map |
| 3m7nG | 3 | 0.9878 | 99.4 | 0.175 | Contact Map |
| 3b4tA | 6 | 1 | 99.4 | 0.177 | Contact Map |
| 4ifdA | 1 | 1 | 99.4 | 0.179 | Contact Map |
| 2nn6C | 1 | 1 | 99.4 | 0.181 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)