| TGS |
| ID: | 1459775226 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 69 (66) | ||
| Sequences: | 2230 (984) | ||
| Seq/Len: | 33.788 | ||
| Nf(neff/√len): | 121.1 |
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: 33.788).
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 |
| 29_Y | 37_H | 5.212 | 1.00 |
| 45_G | 59_D | 3.683 | 1.00 |
| 43_K | 62_E | 2.881 | 1.00 |
| 35_V | 65_T | 2.702 | 1.00 |
| 5_R | 17_D | 2.565 | 1.00 |
| 10_T | 16_V | 2.477 | 1.00 |
| 24_P | 42_A | 2.140 | 1.00 |
| 44_I | 49_V | 1.949 | 1.00 |
| 8_V | 55_L | 1.838 | 1.00 |
| 21_G | 54_Q | 1.641 | 1.00 |
| 39_C | 51_F | 1.631 | 1.00 |
| 29_Y | 36_G | 1.548 | 1.00 |
| 16_V | 30_H | 1.496 | 1.00 |
| 53_Y | 56_Q | 1.487 | 1.00 |
| 40_I | 66_Q | 1.439 | 1.00 |
| 22_S | 26_D | 1.436 | 1.00 |
| 5_R | 8_V | 1.427 | 1.00 |
| 53_Y | 59_D | 1.387 | 0.99 |
| 25_L | 39_C | 1.325 | 0.99 |
| 55_L | 61_I | 1.312 | 0.99 |
| 41_G | 64_I | 1.310 | 0.99 |
| 7_Y | 15_V | 1.256 | 0.99 |
| 34_D | 38_R | 1.209 | 0.98 |
| 38_R | 65_T | 1.207 | 0.98 |
| 5_R | 60_Q | 1.198 | 0.98 |
| 49_V | 53_Y | 1.158 | 0.97 |
| 42_A | 49_V | 1.084 | 0.96 |
| 41_G | 48_I | 1.049 | 0.94 |
| 18_L | 22_S | 1.047 | 0.94 |
| 2_F | 20_A | 1.037 | 0.94 |
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 | |
| 2ekiA | 1 | 0.9855 | 99.6 | 0.268 | Contact Map |
| 1wxqA | 1 | 0.942 | 99.5 | 0.326 | Contact Map |
| 3hvzA | 6 | 0.9275 | 99.3 | 0.388 | Contact Map |
| 1nyrA | 2 | 0.971 | 99 | 0.479 | Contact Map |
| 2kmmA | 1 | 0.9565 | 98.9 | 0.49 | Contact Map |
| 1ni3A | 1 | 0.913 | 98.8 | 0.505 | Contact Map |
| 1wwtA | 1 | 1 | 98.8 | 0.506 | Contact Map |
| 3j7y7 | 1 | 1 | 98.8 | 0.509 | Contact Map |
| 1tkeA | 1 | 0.942 | 98.7 | 0.525 | Contact Map |
| 4ce4c | 1 | 0.8986 | 98.6 | 0.543 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)