| VgrG 609-765 |
| ID: | 1490184681 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 157 (149) | ||
| Sequences: | 1106 (705.7) | ||
| Seq/Len: | 7.423 | ||
| Nf(neff/√len): | 57.8 |
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: 7.423).
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 |
| 126_A | 139_C | 3.615 | 1.00 |
| 127_Y | 138_G | 3.474 | 1.00 |
| 98_S | 102_L | 3.440 | 1.00 |
| 47_S | 51_T | 3.223 | 1.00 |
| 127_Y | 136_E | 3.109 | 1.00 |
| 38_S | 43_V | 2.741 | 1.00 |
| 31_A | 39_G | 2.698 | 1.00 |
| 118_E | 131_S | 2.575 | 1.00 |
| 101_N | 109_G | 2.316 | 1.00 |
| 110_K | 118_E | 2.216 | 1.00 |
| 129_K | 136_E | 2.128 | 1.00 |
| 118_E | 129_K | 2.020 | 1.00 |
| 75_G | 92_D | 1.858 | 1.00 |
| 131_S | 134_N | 1.808 | 1.00 |
| 147_S | 150_M | 1.746 | 1.00 |
| 67_V | 71_S | 1.741 | 1.00 |
| 134_N | 139_C | 1.640 | 1.00 |
| 120_I | 129_K | 1.633 | 1.00 |
| 31_A | 34_L | 1.615 | 1.00 |
| 63_A | 71_S | 1.610 | 1.00 |
| 93_D | 106_S | 1.576 | 1.00 |
| 13_L | 19_L | 1.454 | 0.99 |
| 44_G | 52_D | 1.448 | 0.99 |
| 76_M | 85_V | 1.441 | 0.99 |
| 81_A | 91_S | 1.410 | 0.99 |
| 126_A | 140_P | 1.377 | 0.99 |
| 99_Q | 108_E | 1.331 | 0.98 |
| 145_L | 150_M | 1.301 | 0.98 |
| 119_L | 123_C | 1.281 | 0.98 |
| 18_M | 25_G | 1.274 | 0.98 |
| 93_D | 103_D | 1.263 | 0.97 |
| 30_S | 39_G | 1.259 | 0.97 |
| 129_K | 138_G | 1.256 | 0.97 |
| 23_P | 26_I | 1.245 | 0.97 |
| 84_R | 93_D | 1.212 | 0.96 |
| 77_Q | 86_N | 1.165 | 0.95 |
| 55_A | 59_F | 1.156 | 0.95 |
| 92_D | 100_Q | 1.155 | 0.95 |
| 84_R | 92_D | 1.154 | 0.95 |
| 51_T | 55_A | 1.125 | 0.94 |
| 53_I | 59_F | 1.118 | 0.94 |
| 110_K | 120_I | 1.117 | 0.94 |
| 28_M | 36_I | 1.115 | 0.94 |
| 59_F | 63_A | 1.114 | 0.94 |
| 112_T | 120_I | 1.104 | 0.93 |
| 57_Q | 65_G | 1.103 | 0.93 |
| 79_L | 86_N | 1.102 | 0.93 |
| 132_G | 140_P | 1.088 | 0.93 |
| 89_A | 94_L | 1.084 | 0.92 |
| 28_M | 34_L | 1.080 | 0.92 |
| 63_A | 67_V | 1.074 | 0.92 |
| 124_G | 131_S | 1.074 | 0.92 |
| 137_L | 143_I | 1.068 | 0.92 |
| 86_N | 95_S | 1.068 | 0.92 |
| 133_G | 136_E | 1.066 | 0.92 |
| 74_Q | 78_L | 1.058 | 0.91 |
| 126_A | 132_G | 1.056 | 0.91 |
| 30_S | 34_L | 1.055 | 0.91 |
| 126_A | 133_G | 1.051 | 0.91 |
| 84_R | 95_S | 1.035 | 0.90 |
| 136_E | 156_T | 1.034 | 0.90 |
| 146_K | 156_T | 1.033 | 0.90 |
| 75_G | 80_A | 1.025 | 0.89 |
| 111_V | 119_L | 1.012 | 0.89 |
| 150_M | 154_G | 1.007 | 0.88 |
| 139_C | 147_S | 1.007 | 0.88 |
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 | |
| 4mtkA | 6 | 0.8662 | 96.4 | 0.829 | Contact Map |
| 3a1mA | 6 | 0.6178 | 91.5 | 0.865 | Contact Map |
| 1wthA | 1 | 0.9618 | 90.1 | 0.869 | Contact Map |
| 4ku0A | 3 | 0.586 | 76.3 | 0.89 | Contact Map |
| 4peuA | 1 | 0.9108 | 68.1 | 0.896 | Contact Map |
| 3witA | 1 | 0.4013 | 53.3 | 0.906 | Contact Map |
| 4i84A | 2 | 0.9236 | 43.7 | 0.911 | Contact Map |
| 3vtoA | 6 | 0.5223 | 26.8 | 0.92 | Contact Map |
| 3izoF | 3 | 0 | 19.7 | 0.925 | Contact Map |
| 1rwrA | 1 | 0.828 | 14.5 | 0.929 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)