| cs-test2 |
| ID: | 1402400857 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 267 (242) | ||
| Sequences: | 2013 (1218) | ||
| Seq/Len: | 8.318 | ||
| Nf(neff/√len): | 78.3 |
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: 8.318).
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 |
| 32_L | 233_V | 3.219 | 1.00 |
| 243_D | 246_V | 3.173 | 1.00 |
| 78_K | 117_D | 3.150 | 1.00 |
| 49_E | 84_Y | 2.949 | 1.00 |
| 40_T | 43_E | 2.842 | 1.00 |
| 71_E | 75_K | 2.588 | 1.00 |
| 125_V | 129_I | 2.574 | 1.00 |
| 240_K | 247_E | 2.382 | 1.00 |
| 211_D | 236_G | 2.350 | 1.00 |
| 102_K | 135_Q | 2.346 | 1.00 |
| 206_L | 211_D | 2.155 | 1.00 |
| 123_G | 149_M | 2.111 | 1.00 |
| 210_G | 214_G | 2.033 | 1.00 |
| 47_L | 51_L | 2.026 | 1.00 |
| 32_L | 248_G | 1.980 | 1.00 |
| 233_V | 236_G | 1.954 | 1.00 |
| 127_P | 131_S | 1.913 | 1.00 |
| 54_K | 249_E | 1.908 | 1.00 |
| 221_D | 225_S | 1.889 | 1.00 |
| 246_V | 250_R | 1.812 | 1.00 |
| 123_G | 146_G | 1.771 | 1.00 |
| 130_V | 179_V | 1.745 | 1.00 |
| 62_V | 66_T | 1.736 | 1.00 |
| 206_L | 236_G | 1.728 | 1.00 |
| 186_R | 218_R | 1.702 | 1.00 |
| 128_G | 131_S | 1.684 | 1.00 |
| 33_C | 57_L | 1.677 | 1.00 |
| 201_T | 228_S | 1.671 | 1.00 |
| 58_L | 86_F | 1.619 | 1.00 |
| 64_I | 73_T | 1.615 | 1.00 |
| 182_F | 199_I | 1.605 | 1.00 |
| 176_K | 194_G | 1.604 | 1.00 |
| 146_G | 150_L | 1.595 | 1.00 |
| 221_D | 254_A | 1.581 | 1.00 |
| 128_G | 217_Y | 1.576 | 1.00 |
| 38_V | 47_L | 1.568 | 1.00 |
| 94_F | 112_I | 1.567 | 1.00 |
| 48_V | 58_L | 1.558 | 1.00 |
| 224_V | 231_I | 1.555 | 1.00 |
| 45_L | 76_P | 1.529 | 1.00 |
| 150_L | 154_S | 1.526 | 1.00 |
| 101_V | 129_I | 1.524 | 1.00 |
| 245_K | 249_E | 1.510 | 1.00 |
| 64_I | 68_F | 1.502 | 1.00 |
| 222_D | 225_S | 1.475 | 0.99 |
| 214_G | 239_A | 1.451 | 0.99 |
| 35_S | 234_G | 1.450 | 0.99 |
| 150_L | 153_L | 1.441 | 0.99 |
| 34_A | 237_L | 1.422 | 0.99 |
| 101_V | 133_L | 1.414 | 0.99 |
| 66_T | 94_F | 1.413 | 0.99 |
| 228_S | 231_I | 1.408 | 0.99 |
| 134_K | 138_E | 1.393 | 0.99 |
| 56_C | 86_F | 1.376 | 0.99 |
| 206_L | 251_Y | 1.373 | 0.99 |
| 213_L | 217_Y | 1.372 | 0.99 |
| 167_G | 171_I | 1.369 | 0.99 |
| 131_S | 135_Q | 1.337 | 0.99 |
| 41_T | 76_P | 1.328 | 0.99 |
| 51_L | 58_L | 1.326 | 0.99 |
| 60_T | 77_L | 1.317 | 0.99 |
| 144_P | 150_L | 1.314 | 0.99 |
| 124_A | 171_I | 1.306 | 0.98 |
| 182_F | 197_W | 1.303 | 0.98 |
| 23_K | 27_E | 1.299 | 0.98 |
| 149_M | 155_C | 1.299 | 0.98 |
| 44_L | 80_L | 1.292 | 0.98 |
| 219_T | 222_D | 1.289 | 0.98 |
| 172_A | 182_F | 1.276 | 0.98 |
| 150_L | 155_C | 1.268 | 0.98 |
| 146_G | 149_M | 1.261 | 0.98 |
| 90_E | 116_A | 1.254 | 0.98 |
| 127_P | 174_S | 1.242 | 0.98 |
| 65_L | 80_L | 1.239 | 0.98 |
| 55_I | 248_G | 1.239 | 0.98 |
| 210_G | 250_R | 1.237 | 0.98 |
| 186_R | 204_V | 1.235 | 0.98 |
| 127_P | 177_D | 1.232 | 0.98 |
| 56_C | 248_G | 1.232 | 0.98 |
| 154_S | 217_Y | 1.218 | 0.97 |
| 149_M | 152_E | 1.214 | 0.97 |
| 184_A | 199_I | 1.210 | 0.97 |
| 81_S | 88_L | 1.203 | 0.97 |
| 206_L | 210_G | 1.202 | 0.97 |
| 148_L | 152_E | 1.195 | 0.97 |
| 149_M | 153_L | 1.184 | 0.97 |
| 67_D | 111_R | 1.179 | 0.97 |
| 90_E | 109_V | 1.175 | 0.96 |
| 119_T | 137_A | 1.170 | 0.96 |
| 102_K | 136_A | 1.165 | 0.96 |
| 120_N | 130_V | 1.152 | 0.96 |
| 124_A | 167_G | 1.151 | 0.96 |
| 246_V | 249_E | 1.150 | 0.96 |
| 44_L | 65_L | 1.149 | 0.96 |
| 88_L | 116_A | 1.146 | 0.96 |
| 39_R | 43_E | 1.140 | 0.96 |
| 148_L | 154_S | 1.133 | 0.95 |
| 34_A | 238_F | 1.126 | 0.95 |
| 218_R | 226_T | 1.124 | 0.95 |
| 149_M | 154_S | 1.118 | 0.95 |
| 128_G | 132_G | 1.113 | 0.95 |
| 148_L | 155_C | 1.112 | 0.95 |
| 176_K | 193_E | 1.109 | 0.95 |
| 32_L | 256_W | 1.107 | 0.95 |
| 57_L | 87_L | 1.105 | 0.95 |
| 55_I | 86_F | 1.099 | 0.94 |
| 47_L | 244_A | 1.098 | 0.94 |
| 145_R | 148_L | 1.097 | 0.94 |
| 62_V | 90_E | 1.096 | 0.94 |
| 169_V | 192_D | 1.090 | 0.94 |
| 46_E | 50_A | 1.087 | 0.94 |
| 50_A | 244_A | 1.082 | 0.94 |
| 101_V | 125_V | 1.072 | 0.93 |
| 41_T | 68_F | 1.072 | 0.93 |
| 119_T | 147_L | 1.068 | 0.93 |
| 250_R | 253_K | 1.063 | 0.93 |
| 50_A | 243_D | 1.061 | 0.93 |
| 87_L | 117_D | 1.055 | 0.93 |
| 152_E | 155_C | 1.044 | 0.92 |
| 33_C | 230_I | 1.043 | 0.92 |
| 162_G | 170_D | 1.039 | 0.92 |
| 52_G | 86_F | 1.038 | 0.92 |
| 36_L | 60_T | 1.034 | 0.92 |
| 222_D | 226_T | 1.033 | 0.92 |
| 54_K | 252_R | 1.032 | 0.91 |
| 148_L | 179_V | 1.032 | 0.91 |
| 24_I | 27_E | 1.025 | 0.91 |
| 210_G | 213_L | 1.022 | 0.91 |
| 57_L | 118_I | 1.019 | 0.91 |
| 144_P | 148_L | 1.016 | 0.91 |
| 144_P | 147_L | 1.009 | 0.90 |
| 144_P | 152_E | 1.007 | 0.90 |
| 103_L | 110_Y | 1.005 | 0.90 |
| 63_D | 238_F | 1.002 | 0.90 |
| 103_L | 239_A | 1.001 | 0.90 |
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 | |
| 3g3dA | 2 | 0.9588 | 100 | 0.257 | Contact Map |
| 3gdmA | 2 | 0.9738 | 100 | 0.26 | Contact Map |
| 3ewwA | 2 | 0.9551 | 100 | 0.302 | Contact Map |
| 3l52A | 1 | 0.8764 | 100 | 0.336 | Contact Map |
| 2fdsA | 2 | 0.8727 | 100 | 0.347 | Contact Map |
| 3r89A | 2 | 0.8801 | 100 | 0.354 | Contact Map |
| 3n3mA | 2 | 0.9176 | 100 | 0.369 | Contact Map |
| 3qw4B | 2 | 0.8652 | 100 | 0.37 | Contact Map |
| 4mjzA | 2 | 0.8989 | 100 | 0.376 | Contact Map |
| 2ffcA | 1 | 0.8689 | 100 | 0.392 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)