| test3 |
| ID: | 1516304078 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 79 (65) | ||
| Sequences: | 773 (573) | ||
| Seq/Len: | 11.892 | ||
| Nf(neff/√len): | 71.1 |
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: 11.892).
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 |
| 39_K | 48_N | 4.784 | 1.00 |
| 28_R | 35_E | 3.884 | 1.00 |
| 27_R | 65_F | 3.113 | 1.00 |
| 51_E | 55_N | 2.596 | 1.00 |
| 20_V | 41_K | 2.254 | 1.00 |
| 27_R | 66_M | 2.237 | 1.00 |
| 30_V | 35_E | 2.035 | 1.00 |
| 36_Y | 66_M | 2.020 | 1.00 |
| 27_R | 34_V | 1.971 | 1.00 |
| 22_E | 39_K | 1.958 | 1.00 |
| 52_P | 55_N | 1.894 | 1.00 |
| 37_L | 48_N | 1.656 | 1.00 |
| 61_L | 65_F | 1.564 | 1.00 |
| 58_C | 61_L | 1.542 | 1.00 |
| 56_L | 61_L | 1.500 | 1.00 |
| 45_E | 48_N | 1.460 | 1.00 |
| 19_Y | 43_F | 1.384 | 0.99 |
| 67_K | 70_K | 1.334 | 0.99 |
| 39_K | 45_E | 1.260 | 0.99 |
| 20_V | 38_L | 1.219 | 0.98 |
| 25_L | 45_E | 1.164 | 0.97 |
| 37_L | 50_W | 1.132 | 0.97 |
| 63_S | 67_K | 1.112 | 0.96 |
| 34_V | 38_L | 1.008 | 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 | |
| 1ap0A | 1 | 0.9241 | 99.7 | 0.242 | Contact Map |
| 4qucA | 1 | 0.6962 | 99.7 | 0.245 | Contact Map |
| 2rsoA | 1 | 0.962 | 99.7 | 0.245 | Contact Map |
| 2kvmA | 1 | 0.8987 | 99.7 | 0.249 | Contact Map |
| 3lweA | 2 | 0.7595 | 99.7 | 0.255 | Contact Map |
| 4x3kA | 2 | 0.8101 | 99.7 | 0.261 | Contact Map |
| 2d9uA | 1 | 0.8987 | 99.7 | 0.264 | Contact Map |
| 1g6zA | 1 | 0.8481 | 99.7 | 0.27 | Contact Map |
| 1pdqA | 1 | 0.6456 | 99.7 | 0.272 | Contact Map |
| 2dntA | 1 | 0.9367 | 99.7 | 0.272 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)