| 1ELKA |
| ID: | 1411763351 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 153 (146) | ||
| Sequences: | 683 (426.2) | ||
| Seq/Len: | 4.678 | ||
| Nf(neff/√len): | 35.3 |
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: 4.678).
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 |
| 77_C | 85_F | 3.093 | 1.00 |
| 33_N | 76_T | 2.556 | 1.00 |
| 116_K | 119_N | 2.410 | 1.00 |
| 58_I | 70_A | 2.076 | 1.00 |
| 13_V | 17_I | 2.013 | 1.00 |
| 40_I | 50_A | 1.948 | 1.00 |
| 20_A | 36_I | 1.815 | 1.00 |
| 38_D | 80_N | 1.810 | 1.00 |
| 75_E | 79_K | 1.792 | 1.00 |
| 17_I | 50_A | 1.741 | 1.00 |
| 91_S | 94_F | 1.665 | 0.99 |
| 95_V | 137_V | 1.564 | 0.99 |
| 17_I | 73_V | 1.520 | 0.98 |
| 75_E | 120_L | 1.509 | 0.98 |
| 34_M | 80_N | 1.492 | 0.98 |
| 30_W | 33_N | 1.486 | 0.98 |
| 37_C | 81_C | 1.449 | 0.98 |
| 40_I | 77_C | 1.435 | 0.98 |
| 31_A | 76_T | 1.432 | 0.97 |
| 22_D | 29_D | 1.431 | 0.97 |
| 79_K | 127_A | 1.420 | 0.97 |
| 30_W | 37_C | 1.404 | 0.97 |
| 79_K | 86_H | 1.385 | 0.97 |
| 99_L | 117_V | 1.362 | 0.96 |
| 41_N | 81_C | 1.350 | 0.96 |
| 23_G | 92_Q | 1.342 | 0.96 |
| 25_L | 33_N | 1.339 | 0.96 |
| 38_D | 79_K | 1.334 | 0.96 |
| 75_E | 124_W | 1.316 | 0.95 |
| 61_N | 64_F | 1.309 | 0.95 |
| 71_L | 124_W | 1.276 | 0.94 |
| 79_K | 118_L | 1.242 | 0.93 |
| 71_L | 121_I | 1.237 | 0.93 |
| 14_G | 53_A | 1.216 | 0.92 |
| 75_E | 86_H | 1.207 | 0.92 |
| 57_R | 118_L | 1.201 | 0.91 |
| 30_W | 76_T | 1.197 | 0.91 |
| 49_D | 52_R | 1.196 | 0.91 |
| 138_V | 142_E | 1.191 | 0.91 |
| 30_W | 80_N | 1.182 | 0.90 |
| 128_F | 131_S | 1.179 | 0.90 |
| 19_K | 121_I | 1.177 | 0.90 |
| 78_V | 148_G | 1.173 | 0.90 |
| 47_P | 82_G | 1.171 | 0.90 |
| 28_E | 69_L | 1.162 | 0.89 |
| 18_E | 57_R | 1.155 | 0.89 |
| 54_V | 103_I | 1.135 | 0.88 |
| 47_P | 84_R | 1.123 | 0.87 |
| 100_V | 140_I | 1.120 | 0.87 |
| 68_M | 72_T | 1.112 | 0.87 |
| 65_H | 68_M | 1.099 | 0.86 |
| 128_F | 137_V | 1.096 | 0.85 |
| 9_F | 13_V | 1.092 | 0.85 |
| 68_M | 116_K | 1.090 | 0.85 |
| 148_G | 151_F | 1.090 | 0.85 |
| 113_V | 125_A | 1.082 | 0.84 |
| 67_V | 70_A | 1.081 | 0.84 |
| 87_V | 146_R | 1.079 | 0.84 |
| 43_T | 46_G | 1.059 | 0.83 |
| 36_I | 73_V | 1.054 | 0.82 |
| 15_Q | 19_K | 1.048 | 0.82 |
| 58_I | 66_E | 1.046 | 0.82 |
| 74_L | 97_S | 1.044 | 0.81 |
| 64_F | 67_V | 1.043 | 0.81 |
| 54_V | 74_L | 1.042 | 0.81 |
| 68_M | 87_V | 1.039 | 0.81 |
| 122_Q | 151_F | 1.038 | 0.81 |
| 32_L | 36_I | 1.026 | 0.80 |
| 90_A | 95_V | 1.022 | 0.79 |
| 32_L | 73_V | 1.020 | 0.79 |
| 21_T | 57_R | 1.013 | 0.79 |
| 54_V | 102_T | 1.009 | 0.78 |
| 28_E | 33_N | 1.009 | 0.78 |
| 14_G | 18_E | 1.006 | 0.78 |
| 38_D | 57_R | 1.001 | 0.77 |
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 | |
| 1elkA | 2 | 1 | 100 | 0.035 | Contact Map |
| 3ldzA | 4 | 0.915 | 100 | 0.113 | Contact Map |
| 1x5bA | 1 | 0.9477 | 100 | 0.118 | Contact Map |
| 1juqA | 4 | 0.9542 | 100 | 0.123 | Contact Map |
| 3rruA | 2 | 0.9216 | 100 | 0.134 | Contact Map |
| 1mhqA | 2 | 0.8954 | 100 | 0.146 | Contact Map |
| 1dvpA | 1 | 0.9281 | 100 | 0.171 | Contact Map |
| 3zyqA | 1 | 0.9085 | 100 | 0.177 | Contact Map |
| 3g2sA | 2 | 0.9346 | 100 | 0.185 | Contact Map |
| 1sz9A | 3 | 0.8824 | 98.2 | 0.791 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)