| d3zoyd_ |
| ID: | 1450931114 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 79 (79) | ||
| Sequences: | 14079 (8941.6) | ||
| Seq/Len: | 178.215 | ||
| Nf(neff/√len): | 1006.0 |
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: 178.215).
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 |
| 65_S | 68_D | 3.449 | 1.00 |
| 43_A | 70_K | 3.331 | 1.00 |
| 44_G | 48_G | 2.484 | 1.00 |
| 4_L | 72_L | 2.278 | 1.00 |
| 43_A | 69_A | 2.248 | 1.00 |
| 67_A | 71_A | 2.167 | 1.00 |
| 39_A | 77_L | 2.128 | 1.00 |
| 42_L | 73_A | 2.065 | 1.00 |
| 43_A | 47_K | 2.061 | 1.00 |
| 47_K | 69_A | 1.794 | 1.00 |
| 47_K | 66_D | 1.745 | 1.00 |
| 4_L | 68_D | 1.735 | 1.00 |
| 38_A | 41_Y | 1.676 | 1.00 |
| 73_A | 77_L | 1.658 | 1.00 |
| 2_A | 6_K | 1.640 | 1.00 |
| 2_A | 7_K | 1.613 | 1.00 |
| 68_D | 71_A | 1.571 | 1.00 |
| 39_A | 74_D | 1.462 | 1.00 |
| 45_K | 49_G | 1.411 | 1.00 |
| 75_W | 79_L | 1.391 | 0.99 |
| 45_K | 50_S | 1.379 | 0.99 |
| 71_A | 74_D | 1.367 | 0.99 |
| 66_D | 70_K | 1.281 | 0.99 |
| 4_L | 9_N | 1.279 | 0.99 |
| 28_I | 31_K | 1.270 | 0.99 |
| 46_I | 69_A | 1.175 | 0.98 |
| 3_D | 7_K | 1.163 | 0.97 |
| 9_N | 12_A | 1.162 | 0.97 |
| 40_T | 44_G | 1.158 | 0.97 |
| 39_A | 43_A | 1.147 | 0.97 |
| 5_A | 72_L | 1.134 | 0.97 |
| 64_V | 72_L | 1.114 | 0.96 |
| 27_D | 30_A | 1.113 | 0.96 |
| 46_I | 73_A | 1.096 | 0.96 |
| 69_A | 73_A | 1.093 | 0.96 |
| 43_A | 73_A | 1.061 | 0.95 |
| 22_G | 25_L | 1.057 | 0.95 |
| 40_T | 43_A | 1.040 | 0.94 |
| 67_A | 70_K | 1.014 | 0.93 |
| 39_A | 73_A | 1.012 | 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 | |
| 2exvA | 2 | 0.9873 | 99.4 | 0.103 | Contact Map |
| 3zoxA | 4 | 1 | 99.4 | 0.106 | Contact Map |
| 1aygA | 1 | 1 | 99.4 | 0.106 | Contact Map |
| 1cchA | 1 | 0.9873 | 99.4 | 0.113 | Contact Map |
| 2d0sA | 1 | 0.9747 | 99.3 | 0.148 | Contact Map |
| 4xxlA | 1 | 0.9873 | 99.3 | 0.156 | Contact Map |
| 1w2lA | 1 | 0.9873 | 99.2 | 0.177 | Contact Map |
| 3wfdC | 1 | 1 | 99.2 | 0.181 | Contact Map |
| 1c52A | 1 | 0.9747 | 99.2 | 0.188 | Contact Map |
| 2yevB | 2 | 0.9747 | 99.2 | 0.194 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)