| 1351tk2 |
| ID: | 1489134145 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 44 (37) | ||
| Sequences: | 282 (185.5) | ||
| Seq/Len: | 7.622 | ||
| Nf(neff/√len): | 30.5 |
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: 7.622).
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 |
| 19_N | 23_K | 2.741 | 1.00 |
| 28_K | 44_T | 1.730 | 1.00 |
| 16_S | 20_G | 1.579 | 1.00 |
| 32_C | 40_C | 1.492 | 0.99 |
| 18_C | 22_C | 1.445 | 0.99 |
| 11_A | 20_G | 1.441 | 0.99 |
| 20_G | 24_R | 1.438 | 0.99 |
| 30_G | 40_C | 1.409 | 0.99 |
| 32_C | 42_C | 1.374 | 0.99 |
| 26_G | 41_W | 1.361 | 0.99 |
| 12_V | 22_C | 1.355 | 0.99 |
| 19_N | 29_G | 1.304 | 0.98 |
| 30_G | 42_C | 1.286 | 0.98 |
| 35_F | 38_V | 1.216 | 0.97 |
| 34_S | 38_V | 1.215 | 0.97 |
| 10_G | 17_D | 1.196 | 0.96 |
| 13_N | 29_G | 1.194 | 0.96 |
| 15_T | 23_K | 1.169 | 0.96 |
| 15_T | 31_H | 1.107 | 0.94 |
| 33_G | 39_N | 1.071 | 0.92 |
| 8_V | 21_E | 1.044 | 0.91 |
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 | |
| 1i2uA | 1 | 1 | 98.9 | 0.168 | Contact Map |
| 1gpsA | 1 | 0.9545 | 98 | 0.369 | Contact Map |
| 2lr3A | 1 | 0.9545 | 98 | 0.37 | Contact Map |
| 4uj0A | 2 | 0.9545 | 98 | 0.373 | Contact Map |
| 1n4nA | 1 | 0.9545 | 98 | 0.374 | Contact Map |
| 1mr4A | 1 | 0.9545 | 98 | 0.375 | Contact Map |
| 1bk8A | 1 | 1 | 97.9 | 0.383 | Contact Map |
| 2kskA | 1 | 0.9545 | 97.9 | 0.386 | Contact Map |
| 1ayjA | 1 | 0.9545 | 97.9 | 0.391 | Contact Map |
| 1ti5A | 1 | 0.9318 | 97.9 | 0.391 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)