| SCO3734 |
| ID: | 1517742139 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 117 (108) | ||
| Sequences: | 1127 (790.6) | ||
| Seq/Len: | 10.435 | ||
| Nf(neff/√len): | 76.1 |
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: 10.435).
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 |
| 32_C | 90_V | 2.436 | 1.00 |
| 58_L | 101_R | 2.381 | 1.00 |
| 95_D | 98_A | 2.320 | 1.00 |
| 2_I | 32_C | 2.270 | 1.00 |
| 90_V | 94_V | 2.144 | 1.00 |
| 5_V | 43_V | 1.935 | 1.00 |
| 7_P | 10_E | 1.724 | 1.00 |
| 3_Y | 35_D | 1.709 | 1.00 |
| 8_L | 12_N | 1.692 | 1.00 |
| 1_M | 61_E | 1.684 | 1.00 |
| 60_D | 100_Q | 1.671 | 1.00 |
| 13_A | 16_G | 1.665 | 1.00 |
| 59_L | 99_V | 1.642 | 1.00 |
| 60_D | 63_R | 1.633 | 1.00 |
| 8_L | 104_E | 1.619 | 1.00 |
| 34_P | 70_W | 1.564 | 1.00 |
| 55_V | 104_E | 1.443 | 1.00 |
| 58_L | 103_L | 1.438 | 1.00 |
| 38_T | 85_T | 1.418 | 1.00 |
| 14_G | 96_R | 1.399 | 0.99 |
| 4_H | 19_Y | 1.398 | 0.99 |
| 92_G | 98_A | 1.393 | 0.99 |
| 107_W | 113_A | 1.368 | 0.99 |
| 34_P | 38_T | 1.358 | 0.99 |
| 55_V | 102_V | 1.327 | 0.99 |
| 6_V | 10_E | 1.319 | 0.99 |
| 96_R | 99_V | 1.297 | 0.99 |
| 5_V | 54_L | 1.273 | 0.99 |
| 59_L | 98_A | 1.273 | 0.99 |
| 8_L | 53_P | 1.267 | 0.99 |
| 5_V | 47_Y | 1.263 | 0.99 |
| 11_W | 99_V | 1.240 | 0.98 |
| 72_A | 86_L | 1.240 | 0.98 |
| 44_N | 113_A | 1.236 | 0.98 |
| 64_L | 68_C | 1.233 | 0.98 |
| 59_L | 64_L | 1.232 | 0.98 |
| 71_E | 87_F | 1.228 | 0.98 |
| 40_L | 44_N | 1.218 | 0.98 |
| 32_C | 59_L | 1.218 | 0.98 |
| 6_V | 55_V | 1.206 | 0.98 |
| 43_V | 105_V | 1.204 | 0.98 |
| 12_N | 15_R | 1.192 | 0.98 |
| 15_R | 102_V | 1.167 | 0.97 |
| 71_E | 88_P | 1.154 | 0.97 |
| 15_R | 96_R | 1.142 | 0.97 |
| 4_H | 23_S | 1.114 | 0.96 |
| 7_P | 50_A | 1.107 | 0.96 |
| 22_D | 26_R | 1.094 | 0.96 |
| 2_I | 61_E | 1.088 | 0.96 |
| 5_V | 39_T | 1.055 | 0.95 |
| 11_W | 43_V | 1.044 | 0.94 |
| 33_S | 42_V | 1.040 | 0.94 |
| 20_A | 93_P | 1.039 | 0.94 |
| 1_M | 100_Q | 1.022 | 0.93 |
| 56_A | 105_V | 1.021 | 0.93 |
| 42_V | 47_Y | 1.016 | 0.93 |
| 46_F | 73_A | 1.006 | 0.93 |
| 34_P | 37_E | 1.004 | 0.93 |
| 1_M | 58_L | 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
- 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 | |
| 2o0qA | 1 | 0.9145 | 100 | 0.098 | Contact Map |
| 1wfxA | 1 | 0.7607 | 39.1 | 0.899 | Contact Map |
| 1gff2 | 1 | 0.8974 | 11 | 0.922 | Contact Map |
| 1xqiA | 3 | 0.4615 | 7.8 | 0.928 | Contact Map |
| 4aneA | 6 | 0.4188 | 7.7 | 0.928 | Contact Map |
| 3js9A | 3 | 0.5385 | 7.6 | 0.928 | Contact Map |
| 2bpa2 | 1 | 0.8889 | 7.3 | 0.928 | Contact Map |
| 1wkjA | 2 | 0.4444 | 6.9 | 0.929 | Contact Map |
| 4dz6A | 6 | 0.5641 | 6.7 | 0.93 | Contact Map |
| 1h05A | 1 | 0.359 | 6.6 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)