| CCDPE_Gremlin_20231205 |
| ID: | 1701739678 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 293 (270) | ||
| Sequences: | 12634 (7966.6) | ||
| Seq/Len: | 46.793 | ||
| Nf(neff/√len): | 484.8 |
HHblits Results: (2016_02)
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 |
| 179_K | 206_G | 3.233 | 1.00 |
| 23_E | 58_N | 3.129 | 1.00 |
| 224_P | 227_E | 3.127 | 1.00 |
| 94_K | 143_C | 3.074 | 1.00 |
| 52_K | 56_H | 2.935 | 1.00 |
| 90_T | 139_V | 2.913 | 1.00 |
| 130_V | 172_Q | 2.802 | 1.00 |
| 32_I | 240_S | 2.655 | 1.00 |
| 146_D | 206_G | 2.630 | 1.00 |
| 280_L | 284_R | 2.597 | 1.00 |
| 94_K | 139_V | 2.585 | 1.00 |
| 148_C | 206_G | 2.469 | 1.00 |
| 53_A | 57_G | 2.455 | 1.00 |
| 277_Q | 281_D | 2.452 | 1.00 |
| 19_K | 54_C | 2.424 | 1.00 |
| 212_E | 219_G | 2.420 | 1.00 |
| 168_D | 172_Q | 2.284 | 1.00 |
| 17_D | 20_Y | 2.277 | 1.00 |
| 146_D | 179_K | 2.129 | 1.00 |
| 199_R | 231_A | 2.066 | 1.00 |
| 103_L | 148_C | 2.036 | 1.00 |
| 97_Y | 143_C | 2.028 | 1.00 |
| 54_C | 58_N | 2.011 | 1.00 |
| 86_K | 135_E | 2.004 | 1.00 |
| 54_C | 57_G | 1.960 | 1.00 |
| 55_A | 62_L | 1.938 | 1.00 |
| 212_E | 221_G | 1.879 | 1.00 |
| 93_L | 143_C | 1.867 | 1.00 |
| 83_K | 87_A | 1.866 | 1.00 |
| 220_R | 278_A | 1.851 | 1.00 |
| 138_K | 175_H | 1.836 | 1.00 |
| 167_V | 200_T | 1.822 | 1.00 |
| 96_L | 101_V | 1.812 | 1.00 |
| 49_N | 98_K | 1.791 | 1.00 |
| 127_E | 172_Q | 1.771 | 1.00 |
| 281_D | 285_Y | 1.770 | 1.00 |
| 148_C | 181_M | 1.725 | 1.00 |
| 23_E | 27_K | 1.718 | 1.00 |
| 199_R | 234_D | 1.713 | 1.00 |
| 26_A | 58_N | 1.708 | 1.00 |
| 193_S | 196_G | 1.692 | 1.00 |
| 282_F | 286_V | 1.685 | 1.00 |
| 167_V | 171_K | 1.675 | 1.00 |
| 231_A | 234_D | 1.664 | 1.00 |
| 87_A | 91_D | 1.648 | 1.00 |
| 226_V | 230_E | 1.639 | 1.00 |
| 139_V | 142_A | 1.634 | 1.00 |
| 164_Q | 200_T | 1.602 | 1.00 |
| 50_E | 53_A | 1.599 | 1.00 |
| 93_L | 140_A | 1.594 | 1.00 |
| 4_G | 242_V | 1.573 | 1.00 |
| 126_W | 168_D | 1.571 | 1.00 |
| 22_I | 58_N | 1.564 | 1.00 |
| 82_R | 132_S | 1.548 | 1.00 |
| 137_A | 178_V | 1.548 | 1.00 |
| 138_K | 142_A | 1.546 | 1.00 |
| 19_K | 57_G | 1.540 | 1.00 |
| 90_T | 94_K | 1.526 | 1.00 |
| 141_E | 177_N | 1.513 | 1.00 |
| 91_D | 94_K | 1.509 | 1.00 |
| 28_L | 280_L | 1.501 | 1.00 |
| 24_K | 27_K | 1.495 | 1.00 |
| 2_K | 61_T | 1.481 | 1.00 |
| 124_G | 127_E | 1.459 | 1.00 |
| 20_Y | 23_E | 1.453 | 1.00 |
| 89_Y | 136_V | 1.435 | 1.00 |
| 141_E | 175_H | 1.427 | 1.00 |
| 139_V | 143_C | 1.422 | 1.00 |
| 128_R | 131_E | 1.410 | 1.00 |
| 86_K | 90_T | 1.405 | 0.99 |
| 48_I | 98_K | 1.403 | 0.99 |
| 23_E | 54_C | 1.390 | 0.99 |
| 45_D | 98_K | 1.388 | 0.99 |
| 22_I | 54_C | 1.386 | 0.99 |
| 226_V | 286_V | 1.384 | 0.99 |
| 26_A | 59_G | 1.376 | 0.99 |
| 196_G | 200_T | 1.375 | 0.99 |
| 22_I | 55_A | 1.373 | 0.99 |
| 47_Q | 50_E | 1.372 | 0.99 |
| 274_R | 278_A | 1.353 | 0.99 |
| 53_A | 56_H | 1.349 | 0.99 |
| 19_K | 50_E | 1.349 | 0.99 |
| 151_V | 187_M | 1.330 | 0.99 |
| 79_P | 83_K | 1.326 | 0.99 |
| 90_T | 135_E | 1.292 | 0.99 |
| 83_K | 135_E | 1.286 | 0.99 |
| 93_L | 139_V | 1.286 | 0.99 |
| 126_W | 172_Q | 1.282 | 0.99 |
| 182_L | 187_M | 1.278 | 0.99 |
| 130_V | 134_R | 1.276 | 0.99 |
| 195_G | 227_E | 1.268 | 0.99 |
| 179_K | 204_Y | 1.260 | 0.99 |
| 134_R | 174_D | 1.243 | 0.98 |
| 30_F | 243_M | 1.238 | 0.98 |
| 127_E | 131_E | 1.235 | 0.98 |
| 137_A | 173_V | 1.223 | 0.98 |
| 166_G | 180_V | 1.210 | 0.98 |
| 208_L | 232_L | 1.202 | 0.98 |
| 52_K | 98_K | 1.199 | 0.98 |
| 196_G | 199_R | 1.195 | 0.98 |
| 131_E | 134_R | 1.182 | 0.98 |
| 87_A | 90_T | 1.169 | 0.97 |
| 184_T | 228_I | 1.168 | 0.97 |
| 230_E | 234_D | 1.162 | 0.97 |
| 168_D | 171_K | 1.161 | 0.97 |
| 231_A | 235_I | 1.159 | 0.97 |
| 273_D | 277_Q | 1.151 | 0.97 |
| 19_K | 23_E | 1.151 | 0.97 |
| 96_L | 104_I | 1.151 | 0.97 |
| 131_E | 135_E | 1.149 | 0.97 |
| 183_D | 244_E | 1.148 | 0.97 |
| 24_K | 273_D | 1.147 | 0.97 |
| 2_K | 240_S | 1.139 | 0.97 |
| 90_T | 143_C | 1.133 | 0.97 |
| 32_I | 61_T | 1.128 | 0.97 |
| 74_L | 132_S | 1.126 | 0.97 |
| 49_N | 53_A | 1.115 | 0.96 |
| 94_K | 98_K | 1.111 | 0.96 |
| 102_H | 146_D | 1.110 | 0.96 |
| 141_E | 176_N | 1.110 | 0.96 |
| 90_T | 142_A | 1.109 | 0.96 |
| 93_L | 145_V | 1.108 | 0.96 |
| 55_A | 60_I | 1.107 | 0.96 |
| 25_V | 30_F | 1.106 | 0.96 |
| 50_E | 54_C | 1.105 | 0.96 |
| 27_K | 273_D | 1.102 | 0.96 |
| 103_L | 146_D | 1.101 | 0.96 |
| 144_G | 177_N | 1.096 | 0.96 |
| 137_A | 177_N | 1.095 | 0.96 |
| 140_A | 147_F | 1.091 | 0.96 |
| 82_R | 128_R | 1.083 | 0.96 |
| 94_K | 97_Y | 1.082 | 0.96 |
| 278_A | 281_D | 1.077 | 0.95 |
| 161_N | 165_E | 1.073 | 0.95 |
| 180_V | 201_A | 1.070 | 0.95 |
| 202_G | 235_I | 1.070 | 0.95 |
| 52_K | 100_D | 1.066 | 0.95 |
| 134_R | 138_K | 1.064 | 0.95 |
| 31_D | 284_R | 1.062 | 0.95 |
| 30_F | 280_L | 1.057 | 0.95 |
| 134_R | 173_V | 1.055 | 0.95 |
| 81_I | 84_N | 1.055 | 0.95 |
| 121_D | 124_G | 1.054 | 0.95 |
| 24_K | 28_L | 1.049 | 0.94 |
| 25_V | 33_L | 1.040 | 0.94 |
| 171_K | 204_Y | 1.036 | 0.94 |
| 167_V | 201_A | 1.030 | 0.94 |
| 162_T | 165_E | 1.025 | 0.93 |
| 210_T | 241_V | 1.019 | 0.93 |
| 150_E | 244_E | 1.012 | 0.93 |
| 218_P | 279_A | 1.011 | 0.93 |
| 34_E | 207_H | 1.009 | 0.93 |
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 | |
| 3vniA | 4 | 0.9795 | 100 | 0.104 | Contact Map |
| 2qulA | 4 | 0.9829 | 100 | 0.125 | Contact Map |
| 2hk0A | 4 | 0.9625 | 100 | 0.132 | Contact Map |
| 3vylA | 8 | 0.9659 | 100 | 0.167 | Contact Map |
| 2qw5A | 2 | 0.9522 | 100 | 0.187 | Contact Map |
| 3wqoA | 2 | 0.8874 | 100 | 0.193 | Contact Map |
| 3kwsA | 2 | 0.884 | 100 | 0.197 | Contact Map |
| 1i60A | 1 | 0.9044 | 100 | 0.2 | Contact Map |
| 2zvrA | 2 | 0.8737 | 100 | 0.207 | Contact Map |
| 3qxbA | 4 | 0.9215 | 100 | 0.212 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)