| 1vjx |
| ID: | 1453737223 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 145 (143) | ||
| Sequences: | 810 (693.3) | ||
| Seq/Len: | 5.664 | ||
| Nf(neff/√len): | 58.0 |
HHblits Results: (2015_06)
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: 5.664).
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 |
| 111_K | 127_I | 3.914 | 1.00 |
| 111_K | 124_K | 2.379 | 1.00 |
| 25_S | 37_L | 2.356 | 1.00 |
| 97_I | 134_L | 2.176 | 1.00 |
| 15_E | 47_A | 2.137 | 1.00 |
| 100_E | 133_H | 2.049 | 1.00 |
| 11_I | 47_A | 2.014 | 1.00 |
| 104_I | 127_I | 1.970 | 1.00 |
| 46_H | 100_E | 1.908 | 1.00 |
| 18_E | 22_R | 1.870 | 1.00 |
| 46_H | 133_H | 1.840 | 1.00 |
| 101_K | 105_I | 1.775 | 1.00 |
| 8_T | 54_S | 1.769 | 1.00 |
| 43_E | 130_E | 1.685 | 1.00 |
| 117_S | 121_K | 1.678 | 1.00 |
| 123_V | 126_I | 1.659 | 1.00 |
| 36_F | 92_V | 1.618 | 0.99 |
| 2_K | 5_D | 1.563 | 0.99 |
| 14_E | 100_E | 1.554 | 0.99 |
| 10_A | 106_L | 1.552 | 0.99 |
| 130_E | 133_H | 1.551 | 0.99 |
| 48_E | 52_K | 1.535 | 0.99 |
| 23_E | 27_H | 1.478 | 0.99 |
| 46_H | 130_E | 1.473 | 0.99 |
| 43_E | 46_H | 1.472 | 0.99 |
| 14_E | 46_H | 1.470 | 0.99 |
| 100_E | 130_E | 1.448 | 0.98 |
| 30_G | 34_K | 1.419 | 0.98 |
| 47_A | 51_R | 1.380 | 0.98 |
| 18_E | 44_R | 1.379 | 0.98 |
| 14_E | 133_H | 1.371 | 0.98 |
| 122_T | 126_I | 1.351 | 0.97 |
| 90_K | 94_D | 1.300 | 0.96 |
| 121_K | 125_K | 1.293 | 0.96 |
| 39_L | 89_L | 1.292 | 0.96 |
| 128_D | 131_K | 1.290 | 0.96 |
| 17_G | 104_I | 1.289 | 0.96 |
| 4_S | 54_S | 1.287 | 0.96 |
| 12_R | 16_E | 1.261 | 0.96 |
| 23_E | 26_E | 1.237 | 0.95 |
| 108_Y | 112_D | 1.235 | 0.95 |
| 24_L | 36_F | 1.227 | 0.95 |
| 39_L | 96_A | 1.224 | 0.95 |
| 35_T | 39_L | 1.214 | 0.94 |
| 10_A | 43_E | 1.204 | 0.94 |
| 17_G | 43_E | 1.184 | 0.93 |
| 104_I | 134_L | 1.167 | 0.92 |
| 109_E | 113_G | 1.166 | 0.92 |
| 43_E | 100_E | 1.159 | 0.92 |
| 10_A | 107_Y | 1.155 | 0.92 |
| 91_E | 94_D | 1.143 | 0.91 |
| 17_G | 129_Q | 1.133 | 0.91 |
| 14_E | 130_E | 1.129 | 0.91 |
| 36_F | 110_L | 1.121 | 0.90 |
| 13_L | 129_Q | 1.117 | 0.90 |
| 4_S | 8_T | 1.095 | 0.89 |
| 6_I | 123_V | 1.085 | 0.88 |
| 74_V | 78_T | 1.059 | 0.87 |
| 41_D | 112_D | 1.058 | 0.87 |
| 25_S | 28_F | 1.027 | 0.84 |
| 129_Q | 132_E | 1.013 | 0.83 |
| 14_E | 107_Y | 1.011 | 0.83 |
| 104_I | 108_Y | 1.010 | 0.83 |
| 43_E | 133_H | 1.004 | 0.82 |
| 98_S | 101_K | 1.003 | 0.82 |
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 | |
| 1vjxA | 1 | 1 | 99.8 | 0.274 | Contact Map |
| 2fzfA | 2 | 0.9862 | 99.7 | 0.359 | Contact Map |
| 2oh3A | 1 | 0.9517 | 99.7 | 0.367 | Contact Map |
| 4etrA | 2 | 0.8207 | 99.3 | 0.51 | Contact Map |
| 4am5A | 2 | 0.9034 | 99.3 | 0.51 | Contact Map |
| 4di0A | 2 | 0.8621 | 99.3 | 0.516 | Contact Map |
| 3uoiA | 48 | 0.9034 | 99 | 0.572 | Contact Map |
| 4cvrA | 1 | 0.9034 | 98.9 | 0.578 | Contact Map |
| 1j30A | 2 | 0.8759 | 98.9 | 0.582 | Contact Map |
| 4tofA | 4 | 0.9034 | 98.9 | 0.583 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)