| Tatiana Brailovskaya |
| ID: | 1500661939 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 81 (81) | ||
| Sequences: | 112 (108) | ||
| Seq/Len: | 1.383 | ||
| Nf(neff/√len): | 12.0 |
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: 1.383).
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 |
| 14_F | 22_Q | 2.432 | 1.00 |
| 38_P | 54_P | 2.420 | 1.00 |
| 22_Q | 30_F | 2.347 | 0.99 |
| 14_F | 54_P | 2.275 | 0.99 |
| 22_Q | 54_P | 2.265 | 0.99 |
| 14_F | 30_F | 2.247 | 0.99 |
| 30_F | 54_P | 2.222 | 0.99 |
| 20_F | 28_I | 1.981 | 0.97 |
| 6_F | 14_F | 1.901 | 0.97 |
| 6_F | 30_F | 1.847 | 0.96 |
| 16_A | 32_A | 1.772 | 0.94 |
| 6_F | 38_P | 1.770 | 0.94 |
| 6_F | 22_Q | 1.704 | 0.93 |
| 30_F | 38_P | 1.696 | 0.92 |
| 14_F | 38_P | 1.642 | 0.91 |
| 6_F | 54_P | 1.614 | 0.90 |
| 12_I | 52_S | 1.610 | 0.89 |
| 22_Q | 38_P | 1.586 | 0.89 |
| 44_I | 47_Q | 1.481 | 0.83 |
| 20_F | 68_G | 1.338 | 0.74 |
| 4_I | 20_F | 1.249 | 0.66 |
| 28_I | 68_G | 1.198 | 0.62 |
| 34_F | 42_E | 1.168 | 0.59 |
| 12_I | 36_I | 1.127 | 0.55 |
| 20_F | 52_S | 1.126 | 0.55 |
| 36_I | 52_S | 1.125 | 0.54 |
| 20_F | 36_I | 1.116 | 0.54 |
| 8_S | 27_H | 1.102 | 0.52 |
| 4_I | 36_I | 1.100 | 0.52 |
| 28_I | 36_I | 1.089 | 0.51 |
| 28_I | 44_I | 1.087 | 0.51 |
| 24_N | 58_D | 1.043 | 0.46 |
| 28_I | 52_S | 1.041 | 0.46 |
| 4_I | 28_I | 1.037 | 0.46 |
| 4_I | 68_G | 1.026 | 0.44 |
| 40_G | 60_L | 1.013 | 0.43 |
| 51_T | 78_I | 1.009 | 0.43 |
| 12_I | 20_F | 1.008 | 0.43 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4xtkA | 8 | 0.3951 | 2.1 | 0.927 | Contact Map |
| 1wthA | 1 | 1 | 1.9 | 0.928 | Contact Map |
| 4bouA | 1 | 0.5185 | 1.7 | 0.931 | Contact Map |
| 3syaA | 1 | 0.321 | 1.6 | 0.932 | Contact Map |
| 3spcA | 1 | 0.284 | 1.2 | 0.936 | Contact Map |
| 3mmgA | 2 | 0.8889 | 1.1 | 0.938 | Contact Map |
| 3zfpA | 1 | 0.6914 | 1 | 0.94 | Contact Map |
| 2gixA | 4 | 0.358 | 0.9 | 0.94 | Contact Map |
| 1ho8A | 1 | 0.3457 | 0.9 | 0.94 | Contact Map |
| 1fizL | 1 | 0.1358 | 0.8 | 0.942 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)