| het short |
| ID: | 1490970993 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 80 (80) | ||
| Sequences: | 3454 (2849.2) | ||
| Seq/Len: | 43.175 | ||
| Nf(neff/√len): | 318.6 |
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: 43.175).
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_C | 50_F | 4.127 | 1.00 |
| 65_L | 69_I | 3.774 | 1.00 |
| 3_A | 47_R | 3.162 | 1.00 |
| 41_Q | 45_D | 3.067 | 1.00 |
| 35_I | 52_V | 2.527 | 1.00 |
| 3_A | 42_A | 2.416 | 1.00 |
| 4_I | 79_A | 2.268 | 1.00 |
| 7_H | 35_I | 2.268 | 1.00 |
| 21_L | 55_C | 2.001 | 1.00 |
| 47_R | 80_A | 1.972 | 1.00 |
| 1_P | 80_A | 1.951 | 1.00 |
| 72_M | 76_Y | 1.935 | 1.00 |
| 37_F | 40_D | 1.907 | 1.00 |
| 7_H | 54_T | 1.869 | 1.00 |
| 33_N | 36_R | 1.752 | 1.00 |
| 39_A | 50_F | 1.671 | 1.00 |
| 40_D | 44_R | 1.611 | 1.00 |
| 71_S | 74_R | 1.541 | 1.00 |
| 19_K | 60_S | 1.483 | 1.00 |
| 33_N | 37_F | 1.468 | 1.00 |
| 68_A | 75_W | 1.429 | 1.00 |
| 68_A | 71_S | 1.311 | 0.99 |
| 42_A | 46_G | 1.288 | 0.99 |
| 41_Q | 44_R | 1.280 | 0.99 |
| 18_Y | 22_K | 1.279 | 0.99 |
| 58_D | 64_E | 1.224 | 0.98 |
| 58_D | 61_N | 1.171 | 0.98 |
| 7_H | 34_K | 1.126 | 0.97 |
| 4_I | 75_W | 1.114 | 0.96 |
| 61_N | 64_E | 1.108 | 0.96 |
| 69_I | 72_M | 1.061 | 0.95 |
| 71_S | 75_W | 1.039 | 0.94 |
| 74_R | 78_D | 1.000 | 0.92 |
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 | |
| 3cc1A | 2 | 0.975 | 5.3 | 0.904 | Contact Map |
| 1uasA | 1 | 0.925 | 5.1 | 0.905 | Contact Map |
| 3lrkA | 1 | 0.9 | 3.9 | 0.91 | Contact Map |
| 3a5vA | 1 | 0.9125 | 3.5 | 0.912 | Contact Map |
| 4ol8A | 4 | 0.9375 | 3.1 | 0.915 | Contact Map |
| 1ew3A | 1 | 0.7375 | 2.9 | 0.916 | Contact Map |
| 2l5pA | 1 | 0.75 | 2.7 | 0.917 | Contact Map |
| 2xsaA | 1 | 0.975 | 2.7 | 0.917 | Contact Map |
| 4p7oA | 2 | 0.675 | 2.5 | 0.919 | Contact Map |
| 2yfoA | 1 | 0.9625 | 2.5 | 0.919 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)