| 4ryr |
| ID: | 1501760867 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 151 (125) | ||
| Sequences: | 789 (782.3) | ||
| Seq/Len: | 6.312 | ||
| Nf(neff/√len): | 70.0 |
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: 6.312).
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 |
| 91_F | 104_D | 3.839 | 1.00 |
| 99_F | 148_Y | 2.652 | 1.00 |
| 112_T | 137_S | 2.391 | 1.00 |
| 88_F | 144_S | 2.259 | 1.00 |
| 109_A | 138_A | 2.145 | 1.00 |
| 62_I | 123_S | 2.130 | 1.00 |
| 43_M | 47_M | 2.067 | 1.00 |
| 38_W | 142_Y | 2.024 | 1.00 |
| 102_T | 145_W | 2.001 | 1.00 |
| 115_L | 130_L | 1.911 | 1.00 |
| 53_F | 85_N | 1.865 | 1.00 |
| 60_V | 78_F | 1.817 | 1.00 |
| 108_V | 133_Y | 1.798 | 1.00 |
| 105_C | 137_S | 1.784 | 1.00 |
| 85_N | 108_V | 1.649 | 1.00 |
| 85_N | 133_Y | 1.639 | 1.00 |
| 45_I | 140_A | 1.624 | 1.00 |
| 84_F | 107_L | 1.592 | 0.99 |
| 115_L | 119_S | 1.584 | 0.99 |
| 81_N | 111_T | 1.581 | 0.99 |
| 109_A | 141_T | 1.559 | 0.99 |
| 78_F | 82_Y | 1.485 | 0.99 |
| 102_T | 144_S | 1.471 | 0.99 |
| 134_F | 138_A | 1.425 | 0.99 |
| 84_F | 111_T | 1.366 | 0.98 |
| 81_N | 133_Y | 1.345 | 0.98 |
| 88_F | 92_Q | 1.343 | 0.98 |
| 84_F | 104_D | 1.325 | 0.98 |
| 114_L | 118_F | 1.306 | 0.97 |
| 49_W | 52_L | 1.297 | 0.97 |
| 52_L | 140_A | 1.296 | 0.97 |
| 77_L | 114_L | 1.286 | 0.97 |
| 44_T | 48_I | 1.265 | 0.96 |
| 52_L | 139_F | 1.243 | 0.96 |
| 47_M | 51_V | 1.214 | 0.95 |
| 62_I | 65_N | 1.199 | 0.95 |
| 45_I | 49_W | 1.195 | 0.95 |
| 87_A | 90_Y | 1.188 | 0.94 |
| 81_N | 85_N | 1.174 | 0.94 |
| 109_A | 137_S | 1.171 | 0.94 |
| 77_L | 111_T | 1.158 | 0.93 |
| 58_L | 61_A | 1.151 | 0.93 |
| 45_I | 88_F | 1.080 | 0.90 |
| 29_W | 39_T | 1.079 | 0.90 |
| 54_G | 58_L | 1.077 | 0.90 |
| 101_A | 104_D | 1.070 | 0.89 |
| 40_P | 139_F | 1.060 | 0.89 |
| 29_W | 98_L | 1.052 | 0.88 |
| 116_I | 127_A | 1.048 | 0.88 |
| 42_G | 140_A | 1.041 | 0.88 |
| 49_W | 136_W | 1.034 | 0.87 |
| 46_G | 140_A | 1.028 | 0.87 |
| 34_E | 150_I | 1.025 | 0.86 |
| 29_W | 33_L | 1.023 | 0.86 |
| 38_W | 68_G | 1.005 | 0.85 |
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 | |
| 4ryoA | 1 | 0 | 100 | 0.076 | Contact Map |
| 4uc1A | 3 | 0.9801 | 100 | 0.114 | Contact Map |
| 2mgyA | 1 | 1 | 100 | 0.148 | Contact Map |
| 4i0uA | 10 | 0.3775 | 5 | 0.929 | Contact Map |
| 4ev6A | 5 | 0.3907 | 4.9 | 0.93 | Contact Map |
| 4qncA | 2 | 0.543 | 2.5 | 0.939 | Contact Map |
| 4n7wA | 2 | 0.3377 | 2.3 | 0.94 | Contact Map |
| 4phzK | 3 | 0.7748 | 1.7 | 0.944 | Contact Map |
| 4qndA | 1 | 0.6291 | 1.6 | 0.945 | Contact Map |
| 1yewC | 3 | 0.6291 | 1.5 | 0.946 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)