| ssn8 |
| ID: | 1517351559 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 57 (56) | ||
| Sequences: | 527 (444) | ||
| Seq/Len: | 9.411 | ||
| Nf(neff/√len): | 59.3 |
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: 9.411).
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 |
| 11_R | 51_I | 2.503 | 1.00 |
| 12_A | 16_S | 2.278 | 1.00 |
| 9_A | 15_V | 1.988 | 1.00 |
| 10_D | 14_L | 1.936 | 1.00 |
| 25_Q | 34_G | 1.828 | 1.00 |
| 25_Q | 35_R | 1.784 | 1.00 |
| 4_R | 8_V | 1.766 | 1.00 |
| 10_D | 15_V | 1.749 | 1.00 |
| 16_S | 21_L | 1.633 | 1.00 |
| 27_V | 33_D | 1.628 | 1.00 |
| 43_T | 46_D | 1.624 | 1.00 |
| 16_S | 22_L | 1.608 | 1.00 |
| 14_L | 44_P | 1.511 | 1.00 |
| 23_T | 26_Q | 1.499 | 1.00 |
| 15_V | 19_T | 1.472 | 1.00 |
| 47_I | 51_I | 1.461 | 1.00 |
| 11_R | 52_A | 1.439 | 1.00 |
| 6_Q | 15_V | 1.408 | 0.99 |
| 28_K | 31_Q | 1.387 | 0.99 |
| 3_T | 6_Q | 1.367 | 0.99 |
| 27_V | 32_R | 1.325 | 0.99 |
| 17_A | 24_G | 1.289 | 0.99 |
| 8_V | 12_A | 1.242 | 0.98 |
| 46_D | 50_A | 1.237 | 0.98 |
| 39_Y | 42_M | 1.235 | 0.98 |
| 50_A | 54_V | 1.190 | 0.98 |
| 47_I | 50_A | 1.035 | 0.93 |
| 7_L | 10_D | 1.029 | 0.93 |
| 48_K | 52_A | 1.005 | 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 | |
| 1hywA | 1 | 1 | 99.1 | 0.061 | Contact Map |
| 2y7cA | 1 | 1 | 7.3 | 0.817 | Contact Map |
| 3mq9A | 8 | 1 | 6.2 | 0.823 | Contact Map |
| 2xr1A | 2 | 1 | 5.3 | 0.829 | Contact Map |
| 3af5A | 1 | 0.9298 | 5 | 0.83 | Contact Map |
| 2p17A | 1 | 0 | 3 | 0.848 | Contact Map |
| 1tksA | 2 | 0.8947 | 2.8 | 0.85 | Contact Map |
| 3rx6A | 1 | 0.7895 | 2.6 | 0.853 | Contact Map |
| 1vpyA | 1 | 0.8772 | 2.6 | 0.853 | Contact Map |
| 1vpqA | 1 | 0.8596 | 2.5 | 0.854 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)