| ont3 |
| ID: | 1500030776 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 130 (125) | ||
| Sequences: | 333 (218.7) | ||
| Seq/Len: | 2.664 | ||
| Nf(neff/√len): | 19.6 |
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: 2.664).
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 |
| 45_F | 79_A | 2.764 | 1.00 |
| 86_W | 92_N | 2.548 | 1.00 |
| 41_A | 82_V | 2.404 | 1.00 |
| 33_H | 97_A | 2.002 | 0.99 |
| 83_M | 99_V | 1.890 | 0.99 |
| 84_S | 100_K | 1.856 | 0.99 |
| 37_D | 100_K | 1.823 | 0.99 |
| 32_T | 97_A | 1.820 | 0.99 |
| 70_F | 74_I | 1.816 | 0.99 |
| 48_P | 74_I | 1.710 | 0.98 |
| 63_Y | 95_A | 1.630 | 0.97 |
| 119_P | 122_V | 1.607 | 0.97 |
| 22_C | 25_W | 1.516 | 0.95 |
| 16_Y | 71_A | 1.515 | 0.95 |
| 32_T | 101_V | 1.513 | 0.95 |
| 17_A | 30_I | 1.503 | 0.95 |
| 17_A | 21_Y | 1.462 | 0.94 |
| 55_M | 67_I | 1.423 | 0.92 |
| 116_P | 123_A | 1.394 | 0.91 |
| 71_A | 75_L | 1.391 | 0.91 |
| 38_A | 85_I | 1.352 | 0.90 |
| 97_A | 101_V | 1.341 | 0.89 |
| 69_L | 106_A | 1.315 | 0.88 |
| 74_I | 103_T | 1.306 | 0.87 |
| 20_G | 25_W | 1.274 | 0.85 |
| 40_I | 104_A | 1.274 | 0.85 |
| 17_A | 23_L | 1.254 | 0.84 |
| 30_I | 88_L | 1.248 | 0.84 |
| 70_F | 107_S | 1.229 | 0.83 |
| 23_L | 94_G | 1.216 | 0.82 |
| 49_L | 106_A | 1.194 | 0.80 |
| 74_I | 77_C | 1.184 | 0.79 |
| 66_M | 106_A | 1.171 | 0.78 |
| 17_A | 88_L | 1.161 | 0.77 |
| 59_E | 118_I | 1.148 | 0.76 |
| 126_S | 130_L | 1.132 | 0.75 |
| 73_F | 81_H | 1.131 | 0.75 |
| 81_H | 107_S | 1.121 | 0.74 |
| 55_M | 64_G | 1.117 | 0.73 |
| 20_G | 23_L | 1.086 | 0.70 |
| 38_A | 61_I | 1.083 | 0.70 |
| 12_F | 15_S | 1.080 | 0.70 |
| 76_A | 108_V | 1.080 | 0.70 |
| 19_H | 25_W | 1.071 | 0.69 |
| 74_I | 80_T | 1.067 | 0.68 |
| 29_L | 88_L | 1.067 | 0.68 |
| 28_A | 98_V | 1.053 | 0.67 |
| 89_W | 93_Y | 1.053 | 0.67 |
| 48_P | 77_C | 1.043 | 0.66 |
| 58_R | 125_P | 1.042 | 0.66 |
| 44_Y | 107_S | 1.041 | 0.66 |
| 43_A | 67_I | 1.040 | 0.65 |
| 64_G | 76_A | 1.028 | 0.64 |
| 63_Y | 120_K | 1.022 | 0.63 |
| 23_L | 96_E | 1.020 | 0.63 |
| 26_E | 68_A | 1.016 | 0.63 |
| 121_A | 124_L | 1.009 | 0.62 |
| 103_T | 107_S | 1.008 | 0.62 |
| 8_L | 12_F | 1.008 | 0.62 |
| 87_T | 91_G | 1.008 | 0.62 |
| 22_C | 107_S | 1.003 | 0.61 |
| 51_L | 67_I | 1.002 | 0.61 |
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 | |
| 2kdrX | 1 | 0.2154 | 1.4 | 0.954 | Contact Map |
| 2l34A | 2 | 0.2538 | 1 | 0.958 | Contact Map |
| 2jwaA | 2 | 0.3308 | 0.9 | 0.959 | Contact Map |
| 2xq2A | 1 | 0.6769 | 0.9 | 0.959 | Contact Map |
| 2ks1B | 1 | 0.3308 | 0.8 | 0.961 | Contact Map |
| 2mc7A | 1 | 0.2308 | 0.8 | 0.961 | Contact Map |
| 2lq0A | 1 | 0.1923 | 0.7 | 0.962 | Contact Map |
| 2hi7B | 1 | 0.2692 | 0.7 | 0.962 | Contact Map |
| 4xnjA | 1 | 0 | 0.7 | 0.963 | Contact Map |
| 4z0nA | 1 | 0.3615 | 0.6 | 0.964 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)