| test |
| ID: | 1512494509 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 89 (88) | ||
| Sequences: | 986 (709) | ||
| Seq/Len: | 11.205 | ||
| Nf(neff/√len): | 75.6 |
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: 11.205).
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 |
| 17_H | 30_Y | 3.838 | 1.00 |
| 12_S | 15_D | 2.541 | 1.00 |
| 31_G | 36_A | 2.220 | 1.00 |
| 33_N | 36_A | 2.198 | 1.00 |
| 18_Q | 32_E | 2.020 | 1.00 |
| 16_L | 34_L | 1.966 | 1.00 |
| 7_G | 53_W | 1.744 | 1.00 |
| 34_L | 69_S | 1.719 | 1.00 |
| 53_W | 59_S | 1.681 | 1.00 |
| 21_K | 32_E | 1.673 | 1.00 |
| 37_L | 73_V | 1.644 | 1.00 |
| 16_L | 70_V | 1.633 | 1.00 |
| 56_F | 67_A | 1.621 | 1.00 |
| 16_L | 20_L | 1.606 | 1.00 |
| 10_I | 16_L | 1.593 | 1.00 |
| 59_S | 64_E | 1.567 | 1.00 |
| 37_L | 41_L | 1.511 | 1.00 |
| 31_G | 39_D | 1.482 | 1.00 |
| 29_Y | 40_C | 1.479 | 1.00 |
| 11_R | 15_D | 1.477 | 1.00 |
| 6_N | 55_Q | 1.469 | 1.00 |
| 38_W | 42_T | 1.459 | 1.00 |
| 8_E | 55_Q | 1.456 | 1.00 |
| 63_T | 66_G | 1.398 | 0.99 |
| 4_V | 54_R | 1.364 | 0.99 |
| 19_T | 22_K | 1.327 | 0.99 |
| 13_I | 35_D | 1.273 | 0.99 |
| 42_T | 77_A | 1.201 | 0.98 |
| 7_G | 19_T | 1.200 | 0.98 |
| 9_Q | 19_T | 1.200 | 0.98 |
| 41_L | 73_V | 1.192 | 0.98 |
| 36_A | 39_D | 1.177 | 0.98 |
| 5_I | 53_W | 1.148 | 0.97 |
| 21_K | 30_Y | 1.141 | 0.97 |
| 26_L | 40_C | 1.104 | 0.96 |
| 18_Q | 21_K | 1.101 | 0.96 |
| 38_W | 73_V | 1.087 | 0.96 |
| 34_L | 70_V | 1.072 | 0.95 |
| 27_P | 40_C | 1.029 | 0.94 |
| 19_T | 23_E | 1.029 | 0.94 |
| 13_I | 17_H | 1.027 | 0.94 |
| 53_W | 70_V | 1.024 | 0.93 |
| 37_L | 74_F | 1.012 | 0.93 |
| 34_L | 37_L | 1.006 | 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 | |
| 2za4B | 2 | 0.9888 | 99.9 | 0.039 | Contact Map |
| 2cx6A | 2 | 0.9663 | 99.8 | 0.13 | Contact Map |
| 1w5sA | 2 | 1 | 64.1 | 0.829 | Contact Map |
| 4xgcE | 1 | 0.9663 | 62.5 | 0.831 | Contact Map |
| 1vh6A | 2 | 0.8764 | 43.4 | 0.849 | Contact Map |
| 1fnnA | 2 | 0.9663 | 38.5 | 0.853 | Contact Map |
| 4xgcC | 1 | 0.9438 | 38.4 | 0.854 | Contact Map |
| 4xgcA | 1 | 0.8427 | 32.5 | 0.859 | Contact Map |
| 4iwbA | 2 | 0.8652 | 31.4 | 0.86 | Contact Map |
| 2v1uA | 1 | 0.9326 | 27 | 0.865 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)