| Precursor HVI-2 |
| ID: | 1509204043 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 67 (67) | ||
| Sequences: | 778 (645.1) | ||
| Seq/Len: | 11.612 | ||
| Nf(neff/√len): | 78.8 |
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: 11.612).
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 |
| 6_Y | 9_P | 2.562 | 1.00 |
| 14_V | 20_A | 1.884 | 1.00 |
| 56_L | 59_G | 1.732 | 1.00 |
| 15_G | 21_T | 1.648 | 1.00 |
| 6_Y | 15_G | 1.546 | 1.00 |
| 13_K | 19_E | 1.526 | 1.00 |
| 41_W | 45_W | 1.467 | 1.00 |
| 14_V | 17_F | 1.430 | 1.00 |
| 54_H | 58_A | 1.409 | 1.00 |
| 61_S | 64_E | 1.368 | 0.99 |
| 41_W | 46_T | 1.368 | 0.99 |
| 46_T | 49_P | 1.360 | 0.99 |
| 6_Y | 17_F | 1.303 | 0.99 |
| 63_S | 67_A | 1.259 | 0.99 |
| 41_W | 48_L | 1.254 | 0.99 |
| 45_W | 48_L | 1.241 | 0.98 |
| 11_L | 48_L | 1.230 | 0.98 |
| 15_G | 20_A | 1.222 | 0.98 |
| 10_Q | 13_K | 1.220 | 0.98 |
| 14_V | 21_T | 1.202 | 0.98 |
| 17_F | 21_T | 1.190 | 0.98 |
| 47_A | 50_L | 1.183 | 0.98 |
| 5_K | 10_Q | 1.159 | 0.97 |
| 62_L | 65_T | 1.145 | 0.97 |
| 61_S | 66_F | 1.128 | 0.97 |
| 44_P | 47_A | 1.127 | 0.97 |
| 42_Q | 47_A | 1.125 | 0.97 |
| 61_S | 65_T | 1.106 | 0.96 |
| 50_L | 67_A | 1.096 | 0.96 |
| 49_P | 56_L | 1.091 | 0.96 |
| 58_A | 65_T | 1.070 | 0.95 |
| 57_L | 62_L | 1.069 | 0.95 |
| 11_L | 21_T | 1.057 | 0.95 |
| 60_L | 63_S | 1.047 | 0.94 |
| 26_A | 31_E | 1.046 | 0.94 |
| 8_A | 36_F | 1.039 | 0.94 |
| 28_W | 35_V | 1.029 | 0.94 |
| 35_V | 39_F | 1.025 | 0.93 |
| 53_G | 56_L | 1.024 | 0.93 |
| 41_W | 44_P | 1.022 | 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 | |
| 4m5dA | 1 | 1 | 1.5 | 0.819 | Contact Map |
| 1bg1A | 1 | 0.209 | 0.8 | 0.849 | Contact Map |
| 2xqyA | 2 | 0 | 0.7 | 0.849 | Contact Map |
| 4iz6A | 2 | 0.3433 | 0.7 | 0.853 | Contact Map |
| 2p3yA | 2 | 0.209 | 0.6 | 0.859 | Contact Map |
| 3u07A | 3 | 0.2239 | 0.6 | 0.861 | Contact Map |
| 1mukA | 1 | 0.806 | 0.6 | 0.863 | Contact Map |
| 3dmpA | 4 | 0.4478 | 0.6 | 0.863 | Contact Map |
| 2a0uA | 2 | 0.6119 | 0.5 | 0.866 | Contact Map |
| 2laiA | 1 | 0.597 | 0.5 | 0.866 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)