| p16 |
| ID: | 1414218514 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 156 (129) | ||
| Sequences: | 24436 (19850.2) | ||
| Seq/Len: | 189.426 | ||
| Nf(neff/√len): | 1747.7 |
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: 189.426).
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 |
| 94_L | 126_V | 2.647 | 1.00 |
| 46_R | 74_D | 2.364 | 1.00 |
| 28_V | 59_V | 2.319 | 1.00 |
| 78_L | 108_D | 2.230 | 1.00 |
| 60_A | 93_T | 2.156 | 1.00 |
| 24_R | 27_E | 2.005 | 1.00 |
| 73_A | 106_V | 1.775 | 1.00 |
| 112_R | 120_E | 1.734 | 1.00 |
| 112_R | 141_N | 1.725 | 1.00 |
| 30_A | 34_A | 1.715 | 1.00 |
| 23_G | 56_S | 1.694 | 1.00 |
| 91_L | 125_D | 1.682 | 1.00 |
| 62_L | 66_H | 1.681 | 1.00 |
| 25_V | 62_L | 1.659 | 1.00 |
| 83_H | 114_P | 1.655 | 1.00 |
| 89_G | 123_H | 1.616 | 1.00 |
| 91_L | 129_Y | 1.606 | 1.00 |
| 25_V | 58_R | 1.592 | 1.00 |
| 29_R | 62_L | 1.551 | 1.00 |
| 95_V | 129_Y | 1.546 | 1.00 |
| 32_L | 62_L | 1.542 | 1.00 |
| 55_G | 90_F | 1.520 | 1.00 |
| 96_V | 100_A | 1.472 | 1.00 |
| 82_V | 94_L | 1.463 | 1.00 |
| 41_P | 72_C | 1.457 | 1.00 |
| 49_I | 60_A | 1.450 | 1.00 |
| 61_E | 96_V | 1.433 | 1.00 |
| 57_A | 96_V | 1.428 | 1.00 |
| 116_D | 119_E | 1.423 | 1.00 |
| 50_Q | 81_P | 1.421 | 1.00 |
| 129_Y | 133_A | 1.400 | 0.99 |
| 16_L | 28_V | 1.399 | 0.99 |
| 57_A | 92_D | 1.342 | 0.99 |
| 42_N | 46_R | 1.339 | 0.99 |
| 98_H | 129_Y | 1.326 | 0.99 |
| 98_H | 133_A | 1.312 | 0.99 |
| 46_R | 53_M | 1.289 | 0.99 |
| 116_D | 131_R | 1.281 | 0.99 |
| 27_E | 30_A | 1.279 | 0.99 |
| 124_R | 128_R | 1.268 | 0.99 |
| 115_V | 127_A | 1.266 | 0.99 |
| 17_A | 48_P | 1.259 | 0.99 |
| 25_V | 59_V | 1.258 | 0.99 |
| 64_L | 96_V | 1.220 | 0.98 |
| 98_H | 104_L | 1.217 | 0.98 |
| 57_A | 93_T | 1.214 | 0.98 |
| 91_L | 126_V | 1.196 | 0.98 |
| 119_E | 131_R | 1.189 | 0.98 |
| 99_R | 133_A | 1.188 | 0.98 |
| 108_D | 112_R | 1.185 | 0.98 |
| 108_D | 117_L | 1.175 | 0.98 |
| 91_L | 95_V | 1.173 | 0.98 |
| 25_V | 29_R | 1.172 | 0.98 |
| 33_E | 66_H | 1.167 | 0.97 |
| 95_V | 99_R | 1.160 | 0.97 |
| 83_H | 117_L | 1.153 | 0.97 |
| 57_A | 61_E | 1.148 | 0.97 |
| 115_V | 131_R | 1.147 | 0.97 |
| 64_L | 100_A | 1.139 | 0.97 |
| 15_W | 27_E | 1.133 | 0.97 |
| 85_A | 94_L | 1.132 | 0.97 |
| 56_S | 59_V | 1.130 | 0.97 |
| 128_R | 132_A | 1.117 | 0.96 |
| 90_F | 93_T | 1.115 | 0.96 |
| 119_E | 127_A | 1.106 | 0.96 |
| 61_E | 65_L | 1.099 | 0.96 |
| 103_R | 106_V | 1.099 | 0.96 |
| 17_A | 51_V | 1.093 | 0.96 |
| 42_N | 51_V | 1.086 | 0.96 |
| 29_R | 33_E | 1.071 | 0.95 |
| 20_A | 23_G | 1.062 | 0.95 |
| 20_A | 59_V | 1.062 | 0.95 |
| 123_H | 126_V | 1.053 | 0.95 |
| 39_N | 68_A | 1.048 | 0.94 |
| 86_A | 89_G | 1.041 | 0.94 |
| 86_A | 126_V | 1.039 | 0.94 |
| 65_L | 100_A | 1.035 | 0.94 |
| 13_A | 42_N | 1.031 | 0.94 |
| 83_H | 116_D | 1.023 | 0.93 |
| 118_A | 127_A | 1.018 | 0.93 |
| 50_Q | 83_H | 1.002 | 0.92 |
| 119_E | 122_G | 1.000 | 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 | |
| 1bi7B | 1 | 0.8013 | 100 | 0.182 | Contact Map |
| 1n11A | 1 | 0.9936 | 99.9 | 0.226 | Contact Map |
| 4oavB | 2 | 0.9936 | 99.9 | 0.24 | Contact Map |
| 3utmA | 2 | 0.9936 | 99.9 | 0.244 | Contact Map |
| 1oy3D | 1 | 0.9936 | 99.9 | 0.25 | Contact Map |
| 1ihbA | 2 | 0.9231 | 99.9 | 0.258 | Contact Map |
| 4b93B | 1 | 0.9936 | 99.9 | 0.263 | Contact Map |
| 1sw6A | 2 | 0.9744 | 99.9 | 0.265 | Contact Map |
| 4cymD | 3 | 0.9744 | 99.9 | 0.273 | Contact Map |
| 2pnnA | 1 | 0.8654 | 99.9 | 0.277 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)