| rem |
| ID: | 1479042021 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 89 (82) | ||
| Sequences: | 382 (213.4) | ||
| Seq/Len: | 4.659 | ||
| Nf(neff/√len): | 23.6 |
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: 4.659).
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 |
| 18_R | 59_D | 3.781 | 1.00 |
| 69_Q | 72_T | 1.882 | 1.00 |
| 25_P | 54_A | 1.843 | 1.00 |
| 26_E | 35_Q | 1.657 | 0.99 |
| 18_R | 62_H | 1.637 | 0.99 |
| 23_V | 30_I | 1.635 | 0.99 |
| 30_I | 55_V | 1.593 | 0.99 |
| 35_Q | 55_V | 1.563 | 0.99 |
| 19_M | 56_V | 1.525 | 0.98 |
| 19_M | 77_L | 1.483 | 0.98 |
| 61_D | 77_L | 1.472 | 0.98 |
| 72_T | 76_R | 1.448 | 0.98 |
| 31_K | 46_A | 1.447 | 0.98 |
| 18_R | 60_S | 1.435 | 0.97 |
| 10_F | 51_R | 1.404 | 0.97 |
| 18_R | 36_D | 1.345 | 0.96 |
| 37_A | 53_R | 1.340 | 0.96 |
| 34_I | 55_V | 1.331 | 0.96 |
| 53_R | 72_T | 1.309 | 0.95 |
| 13_I | 61_D | 1.262 | 0.94 |
| 53_R | 69_Q | 1.229 | 0.92 |
| 39_D | 58_M | 1.229 | 0.92 |
| 38_R | 45_D | 1.212 | 0.92 |
| 16_A | 63_I | 1.196 | 0.91 |
| 3_I | 17_N | 1.181 | 0.90 |
| 27_S | 53_R | 1.146 | 0.89 |
| 5_L | 21_S | 1.140 | 0.88 |
| 37_A | 69_Q | 1.130 | 0.88 |
| 17_N | 34_I | 1.124 | 0.87 |
| 20_I | 42_M | 1.120 | 0.87 |
| 36_D | 43_L | 1.113 | 0.86 |
| 57_V | 64_I | 1.095 | 0.85 |
| 53_R | 56_V | 1.095 | 0.85 |
| 12_N | 49_G | 1.095 | 0.85 |
| 58_M | 64_I | 1.080 | 0.84 |
| 20_I | 58_M | 1.080 | 0.84 |
| 58_M | 61_D | 1.075 | 0.84 |
| 14_I | 74_A | 1.042 | 0.81 |
| 50_R | 65_L | 1.036 | 0.81 |
| 58_M | 62_H | 1.025 | 0.80 |
| 42_M | 61_D | 1.025 | 0.80 |
| 17_N | 40_R | 1.017 | 0.79 |
| 18_R | 63_I | 1.010 | 0.78 |
| 24_S | 55_V | 1.002 | 0.77 |
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 | |
| 3pjsK | 4 | 0.9326 | 18.8 | 0.921 | Contact Map |
| 2etxA | 2 | 0.3483 | 16.5 | 0.924 | Contact Map |
| 3bwtA | 1 | 0.6404 | 9.8 | 0.931 | Contact Map |
| 1rypL | 2 | 1 | 8.4 | 0.933 | Contact Map |
| 4nr2A | 8 | 0.3483 | 6.5 | 0.936 | Contact Map |
| 4r3oC | 2 | 0.9888 | 5.6 | 0.938 | Contact Map |
| 2jwkA | 2 | 0.4607 | 5.6 | 0.938 | Contact Map |
| 1lnqA | 8 | 0.6966 | 5.3 | 0.939 | Contact Map |
| 2yqrA | 1 | 0.9551 | 5.2 | 0.939 | Contact Map |
| 4r3oD | 2 | 0.9213 | 4.6 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)