| bdu |
| ID: | 1487707339 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 52 (52) | ||
| Sequences: | 267 (111.3) | ||
| Seq/Len: | 5.135 | ||
| Nf(neff/√len): | 15.4 |
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: 5.135).
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 |
| 22_V | 29_I | 1.906 | 1.00 |
| 15_V | 49_M | 1.718 | 1.00 |
| 12_R | 24_D | 1.704 | 1.00 |
| 30_S | 38_Q | 1.655 | 0.99 |
| 8_T | 33_D | 1.582 | 0.99 |
| 1_S | 45_N | 1.548 | 0.99 |
| 4_Y | 33_D | 1.445 | 0.98 |
| 9_N | 47_K | 1.424 | 0.98 |
| 8_T | 41_I | 1.273 | 0.95 |
| 3_N | 18_G | 1.269 | 0.95 |
| 17_E | 21_K | 1.256 | 0.94 |
| 2_S | 27_G | 1.244 | 0.94 |
| 19_K | 26_T | 1.215 | 0.93 |
| 12_R | 34_A | 1.204 | 0.93 |
| 4_Y | 8_T | 1.200 | 0.93 |
| 37_Q | 42_N | 1.183 | 0.92 |
| 18_G | 43_R | 1.176 | 0.92 |
| 17_E | 39_Q | 1.174 | 0.91 |
| 13_T | 50_A | 1.143 | 0.90 |
| 14_I | 27_G | 1.121 | 0.89 |
| 31_Y | 45_N | 1.103 | 0.88 |
| 22_V | 43_R | 1.100 | 0.88 |
| 29_I | 40_Q | 1.093 | 0.87 |
| 21_K | 24_D | 1.087 | 0.87 |
| 7_H | 15_V | 1.080 | 0.86 |
| 15_V | 47_K | 1.062 | 0.85 |
| 23_D | 40_Q | 1.024 | 0.82 |
| 27_G | 31_Y | 1.020 | 0.82 |
| 17_E | 25_E | 1.002 | 0.80 |
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 | |
| 2rb6A | 2 | 1 | 99.8 | -0.003 | Contact Map |
| 2jn0A | 1 | 0.9615 | 99.8 | 0.006 | Contact Map |
| 2ra2A | 6 | 1 | 99.8 | 0.006 | Contact Map |
| 2rd1A | 3 | 1 | 99.8 | 0.011 | Contact Map |
| 3bduA | 7 | 1 | 99.8 | 0.011 | Contact Map |
| 2k57A | 1 | 1 | 99.8 | 0.017 | Contact Map |
| 1qwyA | 1 | 0.9231 | 9.8 | 0.869 | Contact Map |
| 2fgtA | 1 | 0.7885 | 9 | 0.871 | Contact Map |
| 2xvlA | 1 | 0.9615 | 6.3 | 0.88 | Contact Map |
| 4ofqA | 2 | 1 | 5.8 | 0.882 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)