| ff_domain |
| ID: | 1405071951 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 69 (65) | ||
| Sequences: | 113 (66.3) | ||
| Seq/Len: | 1.738 | ||
| Nf(neff/√len): | 8.2 |
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: 1.738).
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 |
| 38_M | 42_I | 2.364 | 1.00 |
| 14_E | 41_I | 2.283 | 1.00 |
| 28_V | 32_A | 2.020 | 0.99 |
| 19_F | 23_L | 1.915 | 0.98 |
| 24_K | 45_P | 1.831 | 0.97 |
| 16_K | 62_A | 1.579 | 0.92 |
| 43_N | 46_R | 1.462 | 0.87 |
| 38_M | 50_L | 1.451 | 0.87 |
| 27_R | 42_I | 1.425 | 0.85 |
| 37_A | 43_N | 1.424 | 0.85 |
| 39_K | 65_V | 1.401 | 0.84 |
| 26_K | 52_K | 1.380 | 0.83 |
| 29_P | 39_K | 1.337 | 0.80 |
| 58_Q | 61_N | 1.323 | 0.79 |
| 22_L | 41_I | 1.306 | 0.78 |
| 42_I | 47_Y | 1.252 | 0.73 |
| 30_S | 55_E | 1.236 | 0.72 |
| 38_M | 47_Y | 1.215 | 0.70 |
| 12_K | 55_E | 1.202 | 0.69 |
| 28_V | 35_E | 1.187 | 0.68 |
| 41_I | 47_Y | 1.186 | 0.67 |
| 56_K | 66_Q | 1.144 | 0.63 |
| 56_K | 59_A | 1.142 | 0.63 |
| 57_K | 61_N | 1.131 | 0.62 |
| 14_E | 44_D | 1.121 | 0.61 |
| 33_S | 60_F | 1.094 | 0.58 |
| 13_E | 35_E | 1.083 | 0.57 |
| 38_M | 49_A | 1.071 | 0.56 |
| 25_E | 46_R | 1.057 | 0.54 |
| 52_K | 56_K | 1.048 | 0.53 |
| 18_A | 26_K | 1.048 | 0.53 |
| 22_L | 31_N | 1.038 | 0.52 |
| 34_W | 66_Q | 1.038 | 0.52 |
| 27_R | 45_P | 1.023 | 0.51 |
| 36_Q | 53_L | 1.015 | 0.50 |
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 | |
| 1uzcA | 1 | 1 | 99.9 | 0.258 | Contact Map |
| 2b7eA | 1 | 0.8261 | 99.8 | 0.346 | Contact Map |
| 2dodA | 1 | 0.9855 | 99.8 | 0.365 | Contact Map |
| 3hfhA | 2 | 0.7681 | 99.7 | 0.429 | Contact Map |
| 2jucA | 1 | 0.7971 | 99.7 | 0.435 | Contact Map |
| 4fqgA | 2 | 0.8986 | 99.6 | 0.47 | Contact Map |
| 2doeA | 1 | 1 | 99.5 | 0.479 | Contact Map |
| 2dofA | 1 | 1 | 99.4 | 0.527 | Contact Map |
| 2cqnA | 1 | 0.942 | 98.6 | 0.658 | Contact Map |
| 2kfdA | 1 | 0.8696 | 72.4 | 0.861 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)