| flip_withoutsignal |
| ID: | 1447701819 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 222 (207) | ||
| Sequences: | 1404 (743.6) | ||
| Seq/Len: | 6.783 | ||
| Nf(neff/√len): | 51.7 |
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: 6.783).
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 |
| 86_I | 112_L | 4.370 | 1.00 |
| 85_K | 89_D | 3.109 | 1.00 |
| 87_Y | 92_Q | 3.023 | 1.00 |
| 46_I | 67_L | 2.635 | 1.00 |
| 109_A | 145_M | 2.487 | 1.00 |
| 99_I | 107_K | 2.440 | 1.00 |
| 100_S | 103_E | 2.439 | 1.00 |
| 45_I | 49_F | 2.325 | 1.00 |
| 86_I | 90_A | 2.231 | 1.00 |
| 63_P | 66_V | 2.159 | 1.00 |
| 53_R | 64_N | 2.145 | 1.00 |
| 143_V | 148_L | 2.129 | 1.00 |
| 55_A | 168_F | 2.118 | 1.00 |
| 47_I | 157_L | 2.089 | 1.00 |
| 80_S | 83_I | 2.034 | 1.00 |
| 92_Q | 96_E | 2.000 | 1.00 |
| 45_I | 78_I | 1.990 | 1.00 |
| 113_R | 145_M | 1.987 | 1.00 |
| 121_R | 124_D | 1.977 | 1.00 |
| 126_A | 130_R | 1.963 | 1.00 |
| 67_L | 71_A | 1.956 | 1.00 |
| 48_V | 217_L | 1.851 | 1.00 |
| 24_V | 28_S | 1.761 | 1.00 |
| 41_S | 78_I | 1.759 | 1.00 |
| 117_L | 140_P | 1.736 | 1.00 |
| 128_F | 154_T | 1.715 | 1.00 |
| 91_Y | 95_S | 1.714 | 1.00 |
| 145_M | 149_L | 1.691 | 1.00 |
| 82_V | 85_K | 1.671 | 1.00 |
| 45_I | 221_F | 1.671 | 1.00 |
| 134_S | 144_P | 1.655 | 1.00 |
| 31_F | 35_I | 1.632 | 1.00 |
| 117_L | 145_M | 1.619 | 1.00 |
| 89_D | 107_K | 1.587 | 1.00 |
| 49_F | 213_L | 1.562 | 1.00 |
| 107_K | 110_Q | 1.553 | 0.99 |
| 123_A | 211_Q | 1.531 | 0.99 |
| 215_G | 219_Q | 1.527 | 0.99 |
| 28_S | 35_I | 1.508 | 0.99 |
| 38_M | 153_V | 1.500 | 0.99 |
| 69_G | 153_V | 1.495 | 0.99 |
| 113_R | 148_L | 1.482 | 0.99 |
| 87_Y | 91_Y | 1.437 | 0.99 |
| 92_Q | 95_S | 1.419 | 0.99 |
| 51_L | 201_L | 1.418 | 0.99 |
| 129_A | 132_A | 1.392 | 0.99 |
| 131_L | 218_A | 1.391 | 0.99 |
| 20_V | 24_V | 1.387 | 0.99 |
| 44_R | 221_F | 1.370 | 0.98 |
| 185_L | 194_T | 1.352 | 0.98 |
| 117_L | 148_L | 1.352 | 0.98 |
| 53_R | 62_P | 1.330 | 0.98 |
| 173_I | 177_V | 1.325 | 0.98 |
| 169_I | 173_I | 1.297 | 0.97 |
| 103_E | 107_K | 1.295 | 0.97 |
| 115_F | 152_Y | 1.284 | 0.97 |
| 109_A | 113_R | 1.273 | 0.97 |
| 108_G | 111_P | 1.232 | 0.96 |
| 51_L | 58_T | 1.219 | 0.96 |
| 85_K | 114_A | 1.210 | 0.96 |
| 39_M | 112_L | 1.207 | 0.96 |
| 60_S | 193_A | 1.172 | 0.95 |
| 103_E | 106_D | 1.171 | 0.95 |
| 90_A | 108_G | 1.162 | 0.94 |
| 189_M | 196_A | 1.160 | 0.94 |
| 158_K | 162_Q | 1.140 | 0.94 |
| 208_D | 211_Q | 1.139 | 0.94 |
| 155_S | 159_T | 1.134 | 0.93 |
| 163_I | 217_L | 1.131 | 0.93 |
| 84_D | 146_R | 1.123 | 0.93 |
| 88_V | 92_Q | 1.119 | 0.93 |
| 18_L | 21_Q | 1.103 | 0.92 |
| 75_T | 83_I | 1.099 | 0.92 |
| 167_I | 207_V | 1.091 | 0.92 |
| 168_F | 172_L | 1.087 | 0.91 |
| 38_M | 70_L | 1.077 | 0.91 |
| 83_I | 91_Y | 1.076 | 0.91 |
| 154_T | 211_Q | 1.061 | 0.90 |
| 28_S | 31_F | 1.056 | 0.90 |
| 129_A | 137_L | 1.055 | 0.90 |
| 122_E | 126_A | 1.038 | 0.89 |
| 144_P | 147_I | 1.026 | 0.88 |
| 34_A | 37_L | 1.025 | 0.88 |
| 87_Y | 90_A | 1.006 | 0.86 |
| 32_L | 191_P | 1.000 | 0.86 |
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 | |
| 1rh5B | 1 | 0.2252 | 5.7 | 0.973 | Contact Map |
| 4w252 | 1 | 0.2523 | 5.4 | 0.973 | Contact Map |
| 3jstA | 2 | 0.1351 | 4.6 | 0.974 | Contact Map |
| 2ww9B | 1 | 0.2703 | 2.8 | 0.977 | Contact Map |
| 1m45B | 1 | 0.1126 | 2.3 | 0.977 | Contact Map |
| 3hxaA | 8 | 0.1532 | 2.3 | 0.978 | Contact Map |
| 1co4A | 1 | 0.0856 | 2.2 | 0.978 | Contact Map |
| 3thiA | 1 | 0.3649 | 1.7 | 0.979 | Contact Map |
| 2f6mA | 2 | 0.2838 | 1.7 | 0.979 | Contact Map |
| 2mk9A | 2 | 0.0856 | 1.3 | 0.98 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)