| T0814-D1 |
| ID: | 1496200845 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 137 (131) | ||
| Sequences: | 292 (227.5) | ||
| Seq/Len: | 2.229 | ||
| Nf(neff/√len): | 19.9 |
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: 2.229).
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 |
| 60_N | 64_T | 4.225 | 1.00 |
| 52_Y | 129_I | 2.413 | 1.00 |
| 18_V | 132_A | 2.103 | 1.00 |
| 44_G | 52_Y | 1.919 | 0.99 |
| 119_V | 130_F | 1.867 | 0.99 |
| 18_V | 40_I | 1.835 | 0.98 |
| 18_V | 38_I | 1.804 | 0.98 |
| 30_I | 136_V | 1.783 | 0.98 |
| 16_L | 40_I | 1.716 | 0.97 |
| 102_L | 109_F | 1.710 | 0.97 |
| 100_L | 117_I | 1.656 | 0.96 |
| 40_I | 132_A | 1.655 | 0.96 |
| 54_Y | 76_G | 1.538 | 0.94 |
| 58_H | 66_S | 1.442 | 0.91 |
| 75_N | 110_K | 1.399 | 0.89 |
| 55_N | 86_A | 1.370 | 0.87 |
| 17_Q | 41_N | 1.364 | 0.87 |
| 13_I | 44_G | 1.359 | 0.87 |
| 48_G | 128_I | 1.340 | 0.86 |
| 84_D | 99_R | 1.325 | 0.85 |
| 75_N | 136_V | 1.315 | 0.84 |
| 31_A | 56_V | 1.293 | 0.83 |
| 82_I | 96_S | 1.288 | 0.82 |
| 57_V | 118_Q | 1.284 | 0.82 |
| 20_V | 38_I | 1.283 | 0.82 |
| 15_T | 32_L | 1.269 | 0.81 |
| 50_T | 121_N | 1.236 | 0.79 |
| 62_D | 66_S | 1.232 | 0.78 |
| 55_N | 118_Q | 1.226 | 0.78 |
| 33_G | 101_L | 1.210 | 0.77 |
| 69_S | 110_K | 1.210 | 0.77 |
| 15_T | 48_G | 1.209 | 0.77 |
| 63_W | 114_N | 1.153 | 0.72 |
| 24_L | 102_L | 1.145 | 0.71 |
| 63_W | 76_G | 1.135 | 0.70 |
| 72_E | 97_N | 1.124 | 0.69 |
| 27_E | 135_S | 1.122 | 0.69 |
| 79_G | 130_F | 1.110 | 0.67 |
| 79_G | 100_L | 1.110 | 0.67 |
| 25_I | 30_I | 1.104 | 0.67 |
| 60_N | 65_Q | 1.097 | 0.66 |
| 102_L | 112_S | 1.096 | 0.66 |
| 54_Y | 104_N | 1.094 | 0.66 |
| 25_I | 29_Y | 1.094 | 0.66 |
| 75_N | 108_Q | 1.090 | 0.65 |
| 51_R | 61_A | 1.087 | 0.65 |
| 119_V | 131_T | 1.082 | 0.65 |
| 85_F | 90_G | 1.080 | 0.64 |
| 17_Q | 126_D | 1.078 | 0.64 |
| 121_N | 127_Q | 1.066 | 0.63 |
| 31_A | 137_V | 1.064 | 0.63 |
| 49_Y | 87_N | 1.062 | 0.62 |
| 51_R | 82_I | 1.058 | 0.62 |
| 118_Q | 128_I | 1.055 | 0.62 |
| 13_I | 52_Y | 1.055 | 0.62 |
| 60_N | 112_S | 1.054 | 0.62 |
| 38_I | 134_F | 1.037 | 0.60 |
| 16_L | 130_F | 1.024 | 0.58 |
| 52_Y | 130_F | 1.016 | 0.57 |
| 70_P | 78_Q | 1.016 | 0.57 |
| 89_I | 129_I | 1.010 | 0.57 |
| 68_L | 94_Q | 1.003 | 0.56 |
| 14_K | 99_R | 1.002 | 0.56 |
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 | |
| 4r7fA | 1 | 1 | 100 | 0.012 | Contact Map |
| 3v9fA | 4 | 0.7591 | 65.3 | 0.925 | Contact Map |
| 4a2lA | 6 | 0.7591 | 62.3 | 0.926 | Contact Map |
| 4dw1A | 1 | 0.8102 | 52.3 | 0.931 | Contact Map |
| 2p9rA | 2 | 0.6934 | 29.1 | 0.94 | Contact Map |
| 3prxB | 2 | 0.8248 | 28.6 | 0.941 | Contact Map |
| 3ottA | 2 | 0.7591 | 27.6 | 0.941 | Contact Map |
| 3hrzA | 1 | 0.8029 | 24.6 | 0.942 | Contact Map |
| 2b39A | 2 | 0.9051 | 19.8 | 0.945 | Contact Map |
| 3cu7A | 2 | 0.9489 | 13.3 | 0.949 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)