| new-cs |
| ID: | 1428458889 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 267 (239) | ||
| Sequences: | 2012 (1211.7) | ||
| Seq/Len: | 8.418 | ||
| Nf(neff/√len): | 78.4 |
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: 8.418).
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 |
| 243_D | 246_V | 3.353 | 1.00 |
| 78_K | 117_D | 3.281 | 1.00 |
| 32_L | 233_V | 3.118 | 1.00 |
| 40_T | 43_E | 2.951 | 1.00 |
| 71_E | 75_K | 2.603 | 1.00 |
| 49_E | 84_Y | 2.444 | 1.00 |
| 102_K | 135_Q | 2.388 | 1.00 |
| 125_V | 129_I | 2.350 | 1.00 |
| 241_G | 247_E | 2.278 | 1.00 |
| 206_L | 211_D | 2.272 | 1.00 |
| 211_D | 236_G | 2.158 | 1.00 |
| 233_V | 236_G | 2.084 | 1.00 |
| 123_G | 149_M | 2.018 | 1.00 |
| 47_L | 51_L | 1.986 | 1.00 |
| 127_P | 131_S | 1.946 | 1.00 |
| 54_K | 249_E | 1.939 | 1.00 |
| 210_G | 214_G | 1.910 | 1.00 |
| 221_D | 225_S | 1.900 | 1.00 |
| 32_L | 248_G | 1.834 | 1.00 |
| 150_L | 154_S | 1.760 | 1.00 |
| 186_R | 218_R | 1.737 | 1.00 |
| 123_G | 146_G | 1.734 | 1.00 |
| 128_G | 131_S | 1.721 | 1.00 |
| 246_V | 250_R | 1.718 | 1.00 |
| 62_V | 66_T | 1.686 | 1.00 |
| 38_V | 47_L | 1.661 | 1.00 |
| 130_V | 179_V | 1.651 | 1.00 |
| 33_C | 57_L | 1.646 | 1.00 |
| 222_D | 225_S | 1.627 | 1.00 |
| 206_L | 236_G | 1.619 | 1.00 |
| 176_K | 194_G | 1.612 | 1.00 |
| 182_F | 199_I | 1.576 | 1.00 |
| 94_F | 112_I | 1.572 | 1.00 |
| 221_D | 254_A | 1.567 | 1.00 |
| 45_L | 76_P | 1.545 | 1.00 |
| 201_T | 228_S | 1.541 | 1.00 |
| 48_V | 58_L | 1.540 | 1.00 |
| 58_L | 86_F | 1.533 | 1.00 |
| 134_K | 138_E | 1.529 | 1.00 |
| 245_K | 249_E | 1.511 | 1.00 |
| 64_I | 73_T | 1.492 | 1.00 |
| 219_T | 222_D | 1.463 | 0.99 |
| 228_S | 231_I | 1.454 | 0.99 |
| 150_L | 153_L | 1.447 | 0.99 |
| 224_V | 231_I | 1.431 | 0.99 |
| 101_V | 133_L | 1.421 | 0.99 |
| 150_L | 155_C | 1.420 | 0.99 |
| 149_M | 155_C | 1.417 | 0.99 |
| 23_N | 27_E | 1.411 | 0.99 |
| 66_T | 94_F | 1.407 | 0.99 |
| 60_T | 77_L | 1.401 | 0.99 |
| 35_S | 234_G | 1.396 | 0.99 |
| 206_L | 210_G | 1.392 | 0.99 |
| 131_S | 135_Q | 1.390 | 0.99 |
| 149_M | 152_E | 1.389 | 0.99 |
| 90_E | 116_A | 1.379 | 0.99 |
| 34_A | 237_L | 1.372 | 0.99 |
| 64_I | 68_F | 1.371 | 0.99 |
| 101_V | 129_I | 1.360 | 0.99 |
| 178_F | 188_M | 1.358 | 0.99 |
| 167_G | 171_I | 1.345 | 0.99 |
| 206_L | 251_Y | 1.344 | 0.99 |
| 109_V | 119_T | 1.336 | 0.99 |
| 149_M | 154_S | 1.323 | 0.99 |
| 41_T | 76_P | 1.321 | 0.99 |
| 56_C | 86_F | 1.318 | 0.99 |
| 210_G | 250_R | 1.316 | 0.99 |
| 127_P | 174_S | 1.314 | 0.99 |
| 172_A | 182_F | 1.314 | 0.99 |
| 214_G | 239_A | 1.294 | 0.98 |
| 51_L | 58_L | 1.284 | 0.98 |
| 148_L | 152_E | 1.283 | 0.98 |
| 54_K | 252_R | 1.280 | 0.98 |
| 182_F | 197_W | 1.279 | 0.98 |
| 250_R | 253_K | 1.278 | 0.98 |
| 146_G | 150_L | 1.273 | 0.98 |
| 149_M | 153_L | 1.271 | 0.98 |
| 146_G | 149_M | 1.270 | 0.98 |
| 152_E | 155_C | 1.269 | 0.98 |
| 39_R | 43_E | 1.253 | 0.98 |
| 148_L | 155_C | 1.239 | 0.98 |
| 50_A | 244_A | 1.229 | 0.98 |
| 184_A | 199_I | 1.227 | 0.98 |
| 124_V | 171_I | 1.223 | 0.97 |
| 249_E | 253_K | 1.201 | 0.97 |
| 87_L | 117_D | 1.187 | 0.97 |
| 55_I | 248_G | 1.180 | 0.97 |
| 148_L | 154_S | 1.176 | 0.97 |
| 169_V | 192_D | 1.169 | 0.96 |
| 44_L | 80_L | 1.166 | 0.96 |
| 46_E | 50_A | 1.163 | 0.96 |
| 128_G | 217_Y | 1.160 | 0.96 |
| 186_R | 204_V | 1.153 | 0.96 |
| 145_R | 148_L | 1.147 | 0.96 |
| 67_D | 111_R | 1.146 | 0.96 |
| 120_N | 130_V | 1.144 | 0.96 |
| 119_T | 147_L | 1.137 | 0.96 |
| 55_I | 86_F | 1.120 | 0.95 |
| 237_L | 241_G | 1.119 | 0.95 |
| 128_G | 132_G | 1.118 | 0.95 |
| 56_C | 248_G | 1.108 | 0.95 |
| 124_V | 167_G | 1.103 | 0.95 |
| 32_L | 256_W | 1.100 | 0.94 |
| 44_L | 65_L | 1.100 | 0.94 |
| 57_L | 87_L | 1.094 | 0.94 |
| 41_T | 68_F | 1.091 | 0.94 |
| 210_G | 213_L | 1.091 | 0.94 |
| 62_V | 90_E | 1.089 | 0.94 |
| 147_L | 180_I | 1.086 | 0.94 |
| 246_V | 249_E | 1.084 | 0.94 |
| 207_D | 212_A | 1.084 | 0.94 |
| 34_A | 238_F | 1.083 | 0.94 |
| 75_K | 79_A | 1.081 | 0.94 |
| 24_I | 27_E | 1.080 | 0.94 |
| 119_T | 137_A | 1.077 | 0.94 |
| 88_L | 116_A | 1.074 | 0.94 |
| 176_K | 193_E | 1.073 | 0.93 |
| 133_L | 136_A | 1.061 | 0.93 |
| 101_V | 125_V | 1.051 | 0.93 |
| 102_K | 136_A | 1.045 | 0.92 |
| 47_L | 244_A | 1.044 | 0.92 |
| 90_E | 109_V | 1.025 | 0.91 |
| 198_L | 229_D | 1.018 | 0.91 |
| 33_C | 230_I | 1.017 | 0.91 |
| 162_G | 170_D | 1.010 | 0.90 |
| 57_L | 118_I | 1.009 | 0.90 |
| 36_L | 60_T | 1.007 | 0.90 |
| 33_C | 200_M | 1.004 | 0.90 |
| 148_L | 179_V | 1.003 | 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 | |
| 3gdmA | 2 | 0.9775 | 100 | 0.143 | Contact Map |
| 3g3dA | 2 | 0.9588 | 100 | 0.245 | Contact Map |
| 3ewwA | 2 | 0.9551 | 100 | 0.281 | Contact Map |
| 2yyuA | 2 | 0.7978 | 100 | 0.327 | Contact Map |
| 4mjzA | 2 | 0.8839 | 100 | 0.336 | Contact Map |
| 3v75A | 1 | 0.9101 | 100 | 0.343 | Contact Map |
| 3n3mA | 2 | 0.9101 | 100 | 0.345 | Contact Map |
| 3qw4B | 2 | 0.8689 | 100 | 0.35 | Contact Map |
| 2fdsA | 2 | 0.8652 | 100 | 0.357 | Contact Map |
| 3qw3A | 2 | 0.839 | 100 | 0.362 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)