| gp6 279-470 |
| ID: | 1431990488 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 192 (158) | ||
| Sequences: | 1479 (1234.8) | ||
| Seq/Len: | 9.361 | ||
| Nf(neff/√len): | 98.2 |
HHblits Results: (2013_03)
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: 9.361).
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 |
| 42_E | 50_L | 3.731 | 1.00 |
| 108_T | 112_E | 3.649 | 1.00 |
| 106_L | 132_S | 3.181 | 1.00 |
| 43_D | 46_R | 2.948 | 1.00 |
| 163_I | 167_D | 2.679 | 1.00 |
| 47_I | 51_G | 2.482 | 1.00 |
| 183_K | 187_L | 2.354 | 1.00 |
| 90_K | 93_Y | 2.215 | 1.00 |
| 119_K | 122_N | 2.089 | 1.00 |
| 144_V | 162_I | 2.014 | 1.00 |
| 93_Y | 129_S | 1.959 | 1.00 |
| 68_D | 84_T | 1.944 | 1.00 |
| 159_E | 163_I | 1.918 | 1.00 |
| 184_S | 187_L | 1.896 | 1.00 |
| 156_Q | 159_E | 1.892 | 1.00 |
| 96_I | 118_L | 1.839 | 1.00 |
| 162_I | 190_V | 1.810 | 1.00 |
| 55_R | 58_Q | 1.807 | 1.00 |
| 185_K | 189_Y | 1.695 | 1.00 |
| 95_F | 131_I | 1.694 | 1.00 |
| 85_F | 97_A | 1.680 | 1.00 |
| 60_R | 66_D | 1.657 | 1.00 |
| 44_I | 47_I | 1.633 | 1.00 |
| 117_Y | 121_Y | 1.589 | 1.00 |
| 112_E | 116_N | 1.588 | 1.00 |
| 97_A | 131_I | 1.563 | 1.00 |
| 111_R | 115_K | 1.483 | 1.00 |
| 71_V | 114_I | 1.474 | 1.00 |
| 63_T | 66_D | 1.469 | 1.00 |
| 142_L | 190_V | 1.456 | 1.00 |
| 111_R | 132_S | 1.456 | 1.00 |
| 164_D | 168_R | 1.448 | 1.00 |
| 160_G | 163_I | 1.436 | 1.00 |
| 106_L | 110_Q | 1.433 | 1.00 |
| 67_Y | 94_A | 1.429 | 0.99 |
| 169_Y | 189_Y | 1.324 | 0.99 |
| 100_P | 110_Q | 1.294 | 0.99 |
| 71_V | 82_V | 1.286 | 0.99 |
| 62_V | 123_L | 1.280 | 0.99 |
| 154_S | 157_W | 1.263 | 0.98 |
| 74_R | 117_Y | 1.263 | 0.98 |
| 98_A | 111_R | 1.251 | 0.98 |
| 60_R | 63_T | 1.240 | 0.98 |
| 114_I | 130_I | 1.232 | 0.98 |
| 51_G | 55_R | 1.215 | 0.98 |
| 68_D | 81_A | 1.207 | 0.98 |
| 79_I | 82_V | 1.196 | 0.98 |
| 70_F | 117_Y | 1.180 | 0.97 |
| 161_Q | 164_D | 1.171 | 0.97 |
| 98_A | 114_I | 1.168 | 0.97 |
| 62_V | 66_D | 1.142 | 0.97 |
| 67_Y | 123_L | 1.141 | 0.97 |
| 142_L | 162_I | 1.122 | 0.96 |
| 96_I | 130_I | 1.120 | 0.96 |
| 112_E | 115_K | 1.106 | 0.96 |
| 75_F | 113_D | 1.105 | 0.96 |
| 106_L | 133_P | 1.101 | 0.95 |
| 138_I | 181_F | 1.095 | 0.95 |
| 30_P | 33_V | 1.089 | 0.95 |
| 157_W | 161_Q | 1.087 | 0.95 |
| 166_I | 186_M | 1.082 | 0.95 |
| 118_L | 128_P | 1.078 | 0.95 |
| 68_D | 83_Q | 1.078 | 0.95 |
| 110_Q | 114_I | 1.076 | 0.95 |
| 83_Q | 97_A | 1.070 | 0.95 |
| 115_K | 128_P | 1.063 | 0.94 |
| 106_L | 111_R | 1.062 | 0.94 |
| 93_Y | 127_T | 1.042 | 0.93 |
| 34_G | 37_G | 1.042 | 0.93 |
| 115_K | 119_K | 1.040 | 0.93 |
| 68_D | 72_S | 1.033 | 0.93 |
| 47_I | 52_T | 1.022 | 0.93 |
| 46_R | 49_E | 1.021 | 0.93 |
| 146_Y | 158_L | 1.020 | 0.92 |
| 62_V | 70_F | 1.013 | 0.92 |
| 37_G | 66_D | 1.011 | 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 | |
| 3h2tA | 2 | 0.6823 | 99.5 | 0.617 | Contact Map |
| 1mdbA | 1 | 0.8021 | 15.2 | 0.929 | Contact Map |
| 2v7bA | 2 | 0.7344 | 15 | 0.93 | Contact Map |
| 3laxA | 1 | 0.5104 | 12.4 | 0.932 | Contact Map |
| 1pg4A | 2 | 0.901 | 10.1 | 0.935 | Contact Map |
| 3c5eA | 1 | 0.7812 | 9.5 | 0.936 | Contact Map |
| 4hrzA | 2 | 0.2865 | 8.4 | 0.937 | Contact Map |
| 2y4oA | 2 | 0.776 | 6.4 | 0.94 | Contact Map |
| 3h0gK | 2 | 0.6198 | 5.8 | 0.942 | Contact Map |
| 3blxB | 8 | 0.5156 | 5.4 | 0.942 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)