| qstr |
| ID: | 1412696946 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 214 (205) | ||
| Sequences: | 31801 (23810) | ||
| Seq/Len: | 155.127 | ||
| Nf(neff/√len): | 1663.0 |
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: 155.127).
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 |
| 20_L | 38_I | 2.743 | 1.00 |
| 172_N | 187_K | 2.678 | 1.00 |
| 158_R | 161_Q | 2.640 | 1.00 |
| 184_F | 187_K | 2.551 | 1.00 |
| 24_I | 28_I | 2.486 | 1.00 |
| 159_E | 196_K | 2.482 | 1.00 |
| 39_E | 63_G | 2.429 | 1.00 |
| 41_E | 63_G | 2.364 | 1.00 |
| 90_L | 110_D | 2.338 | 1.00 |
| 13_L | 43_L | 2.318 | 1.00 |
| 40_P | 64_L | 2.310 | 1.00 |
| 36_P | 52_H | 2.301 | 1.00 |
| 64_L | 71_P | 2.224 | 1.00 |
| 39_E | 42_R | 2.168 | 1.00 |
| 93_E | 113_F | 2.153 | 1.00 |
| 189_H | 192_Q | 2.114 | 1.00 |
| 59_H | 83_L | 2.034 | 1.00 |
| 9_T | 34_P | 1.964 | 1.00 |
| 82_I | 121_I | 1.944 | 1.00 |
| 26_A | 111_T | 1.932 | 1.00 |
| 98_F | 119_G | 1.931 | 1.00 |
| 48_Q | 75_T | 1.930 | 1.00 |
| 54_I | 118_L | 1.903 | 1.00 |
| 20_L | 37_V | 1.858 | 1.00 |
| 164_R | 168_T | 1.836 | 1.00 |
| 14_T | 20_L | 1.790 | 1.00 |
| 165_C | 175_I | 1.784 | 1.00 |
| 69_L | 81_T | 1.773 | 1.00 |
| 57_L | 69_L | 1.710 | 1.00 |
| 13_L | 61_E | 1.702 | 1.00 |
| 44_L | 71_P | 1.695 | 1.00 |
| 60_A | 87_E | 1.662 | 1.00 |
| 27_A | 118_L | 1.662 | 1.00 |
| 102_K | 124_G | 1.655 | 1.00 |
| 71_P | 74_L | 1.636 | 1.00 |
| 83_L | 101_L | 1.628 | 1.00 |
| 87_E | 92_T | 1.627 | 1.00 |
| 139_Y | 149_V | 1.584 | 1.00 |
| 9_T | 36_P | 1.579 | 1.00 |
| 199_V | 208_W | 1.577 | 1.00 |
| 69_L | 83_L | 1.575 | 1.00 |
| 185_T | 189_H | 1.437 | 1.00 |
| 57_L | 68_Q | 1.435 | 1.00 |
| 171_S | 174_Q | 1.429 | 1.00 |
| 55_L | 79_F | 1.422 | 1.00 |
| 190_L | 194_F | 1.408 | 1.00 |
| 83_L | 96_L | 1.392 | 0.99 |
| 156_T | 196_K | 1.376 | 0.99 |
| 47_Y | 72_L | 1.372 | 0.99 |
| 32_N | 119_G | 1.365 | 0.99 |
| 44_L | 68_Q | 1.348 | 0.99 |
| 103_G | 117_G | 1.329 | 0.99 |
| 44_L | 64_L | 1.327 | 0.99 |
| 163_L | 205_A | 1.321 | 0.99 |
| 14_T | 61_E | 1.313 | 0.99 |
| 165_C | 178_N | 1.300 | 0.99 |
| 40_P | 68_Q | 1.296 | 0.99 |
| 10_I | 33_L | 1.295 | 0.99 |
| 73_K | 102_K | 1.286 | 0.99 |
| 54_I | 122_I | 1.278 | 0.99 |
| 43_L | 47_Y | 1.276 | 0.99 |
| 38_I | 42_R | 1.276 | 0.99 |
| 15_T | 58_D | 1.269 | 0.99 |
| 45_R | 49_S | 1.268 | 0.99 |
| 170_A | 178_N | 1.268 | 0.99 |
| 59_H | 66_R | 1.246 | 0.98 |
| 70_G | 95_L | 1.239 | 0.98 |
| 173_M | 177_E | 1.237 | 0.98 |
| 33_L | 119_G | 1.234 | 0.98 |
| 94_D | 97_T | 1.231 | 0.98 |
| 145_Q | 152_T | 1.224 | 0.98 |
| 188_S | 191_Y | 1.221 | 0.98 |
| 66_R | 99_G | 1.214 | 0.98 |
| 13_L | 55_L | 1.212 | 0.98 |
| 60_A | 86_V | 1.199 | 0.98 |
| 23_S | 114_I | 1.193 | 0.98 |
| 89_R | 92_T | 1.188 | 0.98 |
| 190_L | 202_R | 1.180 | 0.98 |
| 41_E | 45_R | 1.164 | 0.97 |
| 12_L | 35_V | 1.154 | 0.97 |
| 71_P | 75_T | 1.154 | 0.97 |
| 11_Y | 43_L | 1.144 | 0.97 |
| 17_P | 20_L | 1.133 | 0.97 |
| 64_L | 67_Q | 1.131 | 0.97 |
| 184_F | 188_S | 1.123 | 0.97 |
| 46_E | 50_D | 1.122 | 0.97 |
| 12_L | 24_I | 1.105 | 0.96 |
| 194_F | 199_V | 1.102 | 0.96 |
| 67_Q | 70_G | 1.092 | 0.96 |
| 36_P | 46_E | 1.086 | 0.96 |
| 23_S | 84_F | 1.077 | 0.95 |
| 46_E | 49_S | 1.076 | 0.95 |
| 168_T | 178_N | 1.067 | 0.95 |
| 11_Y | 52_H | 1.067 | 0.95 |
| 161_Q | 164_R | 1.065 | 0.95 |
| 183_E | 187_K | 1.064 | 0.95 |
| 15_T | 107_A | 1.062 | 0.95 |
| 192_Q | 195_K | 1.061 | 0.95 |
| 121_I | 124_G | 1.060 | 0.95 |
| 11_Y | 47_Y | 1.053 | 0.95 |
| 91_R | 95_L | 1.051 | 0.94 |
| 27_A | 33_L | 1.050 | 0.94 |
| 42_R | 46_E | 1.039 | 0.94 |
| 82_I | 103_G | 1.033 | 0.94 |
| 173_M | 183_E | 1.030 | 0.94 |
| 113_F | 117_G | 1.021 | 0.93 |
| 33_L | 115_A | 1.018 | 0.93 |
| 42_R | 45_R | 1.009 | 0.93 |
| 208_W | 212_N | 1.001 | 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 | |
| 3kloA | 4 | 0.986 | 100 | 0.173 | Contact Map |
| 3c3wA | 2 | 0.9626 | 100 | 0.187 | Contact Map |
| 1a04A | 2 | 0.9393 | 100 | 0.204 | Contact Map |
| 4gvpA | 4 | 0.9486 | 100 | 0.207 | Contact Map |
| 4hyeA | 2 | 0.9159 | 100 | 0.218 | Contact Map |
| 4ldzA | 2 | 0.9019 | 100 | 0.25 | Contact Map |
| 1ys7A | 2 | 0.9626 | 100 | 0.272 | Contact Map |
| 1kgsA | 1 | 0.9579 | 100 | 0.297 | Contact Map |
| 1yioA | 1 | 0.9159 | 100 | 0.298 | Contact Map |
| 4b09A | 12 | 0.8925 | 100 | 0.303 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)