| test |
| ID: | 1490729377 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 89 (84) | ||
| Sequences: | 8978 (5382.5) | ||
| Seq/Len: | 106.881 | ||
| Nf(neff/√len): | 587.3 |
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: 106.881).
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 |
| 54_S | 82_I | 3.956 | 1.00 |
| 58_V | 71_A | 2.621 | 1.00 |
| 37_A | 42_D | 2.610 | 1.00 |
| 30_I | 68_A | 2.601 | 1.00 |
| 46_L | 83_A | 2.547 | 1.00 |
| 29_G | 51_Q | 2.364 | 1.00 |
| 51_Q | 84_Q | 2.234 | 1.00 |
| 31_F | 51_Q | 2.060 | 1.00 |
| 60_L | 63_A | 2.053 | 1.00 |
| 64_S | 67_Q | 1.999 | 1.00 |
| 24_G | 65_H | 1.843 | 1.00 |
| 10_V | 80_T | 1.778 | 1.00 |
| 55_V | 60_L | 1.744 | 1.00 |
| 21_N | 34_F | 1.688 | 1.00 |
| 47_R | 85_Y | 1.673 | 1.00 |
| 54_S | 57_G | 1.659 | 1.00 |
| 38_G | 42_D | 1.540 | 1.00 |
| 50_D | 85_Y | 1.537 | 1.00 |
| 63_A | 71_A | 1.479 | 1.00 |
| 32_I | 46_L | 1.475 | 1.00 |
| 63_A | 67_Q | 1.469 | 1.00 |
| 74_N | 77_Q | 1.435 | 1.00 |
| 21_N | 36_L | 1.392 | 0.99 |
| 25_G | 31_F | 1.371 | 0.99 |
| 23_I | 33_S | 1.345 | 0.99 |
| 60_L | 68_A | 1.333 | 0.99 |
| 7_R | 85_Y | 1.292 | 0.99 |
| 67_Q | 70_I | 1.288 | 0.99 |
| 66_E | 70_I | 1.282 | 0.99 |
| 21_N | 33_S | 1.279 | 0.99 |
| 54_S | 59_D | 1.243 | 0.98 |
| 35_I | 39_G | 1.210 | 0.98 |
| 35_I | 48_K | 1.209 | 0.98 |
| 53_L | 84_Q | 1.176 | 0.98 |
| 8_R | 82_I | 1.165 | 0.97 |
| 65_H | 69_A | 1.158 | 0.97 |
| 10_V | 78_T | 1.115 | 0.96 |
| 12_H | 78_T | 1.068 | 0.95 |
| 22_I | 69_A | 1.040 | 0.94 |
| 35_I | 44_S | 1.000 | 0.92 |
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 | |
| 2xkxA | 2 | 1 | 99 | 0.138 | Contact Map |
| 1z87A | 1 | 1 | 98.9 | 0.176 | Contact Map |
| 1um7A | 1 | 1 | 98.9 | 0.187 | Contact Map |
| 3i4wA | 4 | 0.9888 | 98.9 | 0.19 | Contact Map |
| 1tp5A | 1 | 1 | 98.9 | 0.192 | Contact Map |
| 2dazA | 1 | 1 | 98.9 | 0.192 | Contact Map |
| 1uitA | 1 | 1 | 98.9 | 0.197 | Contact Map |
| 2awxA | 2 | 0.9438 | 98.9 | 0.2 | Contact Map |
| 2fneA | 3 | 1 | 98.8 | 0.2 | Contact Map |
| 1q3oA | 2 | 1 | 98.8 | 0.204 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)