| D3 |
| ID: | 1501854333 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 53 (52) | ||
| Sequences: | 219 (114.3) | ||
| Seq/Len: | 4.212 | ||
| Nf(neff/√len): | 15.9 |
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: 4.212).
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 |
| 8_V | 31_D | 2.185 | 1.00 |
| 40_Q | 45_M | 1.898 | 1.00 |
| 12_E | 15_A | 1.832 | 1.00 |
| 26_T | 41_S | 1.719 | 0.99 |
| 9_Q | 37_L | 1.311 | 0.94 |
| 20_C | 49_C | 1.277 | 0.93 |
| 28_V | 37_L | 1.276 | 0.93 |
| 11_T | 30_N | 1.260 | 0.92 |
| 17_S | 49_C | 1.242 | 0.92 |
| 9_Q | 30_N | 1.238 | 0.91 |
| 34_S | 41_S | 1.234 | 0.91 |
| 24_I | 33_A | 1.225 | 0.91 |
| 12_E | 33_A | 1.195 | 0.89 |
| 18_K | 39_K | 1.190 | 0.89 |
| 28_V | 33_A | 1.178 | 0.89 |
| 6_C | 14_S | 1.170 | 0.88 |
| 19_T | 36_R | 1.154 | 0.87 |
| 36_R | 51_A | 1.147 | 0.87 |
| 15_A | 40_Q | 1.144 | 0.87 |
| 10_T | 39_K | 1.142 | 0.86 |
| 9_Q | 39_K | 1.125 | 0.85 |
| 22_M | 43_L | 1.123 | 0.85 |
| 17_S | 20_C | 1.122 | 0.85 |
| 8_V | 24_I | 1.114 | 0.85 |
| 4_A | 50_E | 1.075 | 0.82 |
| 22_M | 29_T | 1.070 | 0.81 |
| 13_W | 16_C | 1.061 | 0.80 |
| 22_M | 26_T | 1.055 | 0.80 |
| 6_C | 9_Q | 1.047 | 0.79 |
| 4_A | 40_Q | 1.047 | 0.79 |
| 18_K | 34_S | 1.039 | 0.78 |
| 29_T | 46_V | 1.032 | 0.78 |
| 29_T | 32_N | 1.016 | 0.76 |
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 | |
| 4hqfA | 1 | 0.0377 | 97 | 0.688 | Contact Map |
| 3ghmA | 1 | 1 | 96.9 | 0.694 | Contact Map |
| 4okrA | 2 | 0.8868 | 96.5 | 0.706 | Contact Map |
| 3r6bA | 1 | 0.9623 | 96.5 | 0.709 | Contact Map |
| 1vexA | 1 | 0.9245 | 96.3 | 0.712 | Contact Map |
| 2rjqA | 1 | 0.1509 | 96.3 | 0.715 | Contact Map |
| 1szlA | 1 | 0.9811 | 96.2 | 0.715 | Contact Map |
| 4okuA | 2 | 0.8868 | 96 | 0.72 | Contact Map |
| 1lslA | 1 | 0.9434 | 96 | 0.72 | Contact Map |
| 1w0rA | 2 | 1 | 95.5 | 0.732 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)