| BlaR |
| ID: | 1483717107 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 345 (339) | ||
| Sequences: | 1253 (1060.4) | ||
| Seq/Len: | 3.696 | ||
| Nf(neff/√len): | 57.6 |
HHblits Results: (2016_02)
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: 3.696).
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 |
| 184_T | 217_C | 4.356 | 1.00 |
| 205_E | 278_K | 3.372 | 1.00 |
| 225_N | 249_K | 3.034 | 1.00 |
| 43_S | 251_E | 2.930 | 1.00 |
| 219_R | 255_S | 2.768 | 1.00 |
| 17_S | 240_L | 2.667 | 1.00 |
| 23_I | 46_S | 2.556 | 1.00 |
| 202_S | 205_E | 2.480 | 1.00 |
| 13_Q | 235_Y | 2.460 | 1.00 |
| 235_Y | 238_N | 2.391 | 1.00 |
| 40_Y | 252_M | 2.341 | 1.00 |
| 43_S | 244_L | 2.301 | 1.00 |
| 27_K | 251_E | 2.275 | 1.00 |
| 183_I | 193_I | 2.231 | 1.00 |
| 13_Q | 16_L | 2.173 | 1.00 |
| 20_F | 241_V | 2.023 | 1.00 |
| 174_S | 191_Y | 1.976 | 1.00 |
| 228_L | 248_A | 1.954 | 1.00 |
| 12_S | 16_L | 1.924 | 1.00 |
| 27_K | 39_H | 1.923 | 1.00 |
| 232_K | 245_S | 1.884 | 1.00 |
| 231_L | 235_Y | 1.873 | 1.00 |
| 20_F | 244_L | 1.870 | 1.00 |
| 225_N | 252_M | 1.858 | 1.00 |
| 36_V | 258_F | 1.781 | 0.99 |
| 174_S | 193_I | 1.756 | 0.99 |
| 40_Y | 255_S | 1.710 | 0.99 |
| 176_S | 179_I | 1.668 | 0.99 |
| 20_F | 50_L | 1.628 | 0.99 |
| 49_A | 55_I | 1.597 | 0.98 |
| 50_L | 235_Y | 1.588 | 0.98 |
| 244_L | 251_E | 1.581 | 0.98 |
| 158_F | 162_K | 1.560 | 0.98 |
| 303_K | 307_V | 1.507 | 0.97 |
| 164_E | 207_K | 1.478 | 0.97 |
| 58_H | 61_K | 1.441 | 0.96 |
| 173_L | 214_L | 1.439 | 0.96 |
| 225_N | 310_V | 1.433 | 0.96 |
| 275_V | 280_T | 1.424 | 0.96 |
| 13_Q | 237_F | 1.408 | 0.95 |
| 16_L | 235_Y | 1.403 | 0.95 |
| 129_L | 233_I | 1.401 | 0.95 |
| 161_C | 210_L | 1.394 | 0.95 |
| 121_W | 124_G | 1.384 | 0.95 |
| 265_D | 268_L | 1.373 | 0.95 |
| 215_Y | 255_S | 1.365 | 0.94 |
| 149_V | 173_L | 1.349 | 0.94 |
| 171_V | 214_L | 1.332 | 0.93 |
| 13_Q | 17_S | 1.326 | 0.93 |
| 211_L | 264_L | 1.314 | 0.93 |
| 126_A | 130_L | 1.296 | 0.92 |
| 244_L | 248_A | 1.291 | 0.92 |
| 273_G | 306_I | 1.286 | 0.92 |
| 5_F | 9_F | 1.283 | 0.92 |
| 201_F | 205_E | 1.280 | 0.91 |
| 211_L | 263_T | 1.278 | 0.91 |
| 224_I | 248_A | 1.278 | 0.91 |
| 159_H | 162_K | 1.272 | 0.91 |
| 232_K | 242_W | 1.269 | 0.91 |
| 16_L | 49_A | 1.267 | 0.91 |
| 258_F | 306_I | 1.267 | 0.91 |
| 219_R | 252_M | 1.267 | 0.91 |
| 220_K | 223_L | 1.261 | 0.91 |
| 41_Y | 252_M | 1.260 | 0.91 |
| 157_L | 161_C | 1.257 | 0.90 |
| 248_A | 252_M | 1.244 | 0.90 |
| 215_Y | 259_A | 1.243 | 0.90 |
| 273_G | 310_V | 1.236 | 0.89 |
| 229_C | 245_S | 1.235 | 0.89 |
| 186_G | 190_P | 1.233 | 0.89 |
| 335_L | 338_T | 1.231 | 0.89 |
| 153_E | 203_A | 1.228 | 0.89 |
| 231_L | 241_V | 1.228 | 0.89 |
| 177_P | 196_K | 1.220 | 0.89 |
| 247_E | 251_E | 1.216 | 0.88 |
| 27_K | 43_S | 1.211 | 0.88 |
| 20_F | 240_L | 1.204 | 0.88 |
| 2_S | 5_F | 1.203 | 0.88 |
| 20_F | 43_S | 1.202 | 0.88 |
| 124_G | 236_W | 1.202 | 0.88 |
| 43_S | 46_S | 1.201 | 0.88 |
| 260_V | 272_Y | 1.200 | 0.87 |
| 270_L | 310_V | 1.198 | 0.87 |
| 182_P | 195_P | 1.197 | 0.87 |
| 35_T | 39_H | 1.196 | 0.87 |
| 277_L | 306_I | 1.185 | 0.87 |
| 35_T | 221_D | 1.184 | 0.86 |
| 6_F | 118_F | 1.183 | 0.86 |
| 250_T | 304_R | 1.180 | 0.86 |
| 128_M | 233_I | 1.179 | 0.86 |
| 143_K | 193_I | 1.178 | 0.86 |
| 23_I | 27_K | 1.172 | 0.86 |
| 117_F | 126_A | 1.164 | 0.85 |
| 171_V | 217_C | 1.157 | 0.85 |
| 125_V | 233_I | 1.156 | 0.85 |
| 39_H | 252_M | 1.152 | 0.84 |
| 219_R | 259_A | 1.149 | 0.84 |
| 23_I | 43_S | 1.148 | 0.84 |
| 156_S | 160_T | 1.146 | 0.84 |
| 261_L | 309_V | 1.139 | 0.83 |
| 275_V | 279_F | 1.137 | 0.83 |
| 116_A | 126_A | 1.133 | 0.83 |
| 24_I | 251_E | 1.125 | 0.82 |
| 23_I | 251_E | 1.124 | 0.82 |
| 327_F | 335_L | 1.123 | 0.82 |
| 50_L | 53_P | 1.122 | 0.82 |
| 119_A | 123_L | 1.120 | 0.82 |
| 255_S | 258_F | 1.104 | 0.81 |
| 276_I | 280_T | 1.101 | 0.81 |
| 327_F | 331_L | 1.098 | 0.80 |
| 133_L | 137_L | 1.095 | 0.80 |
| 124_G | 128_M | 1.092 | 0.80 |
| 19_F | 46_S | 1.087 | 0.79 |
| 43_S | 50_L | 1.075 | 0.78 |
| 242_W | 245_S | 1.073 | 0.78 |
| 332_G | 336_A | 1.073 | 0.78 |
| 216_H | 253_E | 1.071 | 0.78 |
| 153_E | 157_L | 1.070 | 0.78 |
| 120_V | 124_G | 1.070 | 0.78 |
| 334_I | 338_T | 1.069 | 0.78 |
| 250_T | 301_H | 1.067 | 0.78 |
| 131_A | 229_C | 1.063 | 0.77 |
| 304_R | 308_T | 1.062 | 0.77 |
| 208_C | 275_V | 1.060 | 0.77 |
| 333_A | 336_A | 1.055 | 0.76 |
| 184_T | 222_M | 1.053 | 0.76 |
| 279_F | 306_I | 1.044 | 0.75 |
| 50_L | 251_E | 1.039 | 0.75 |
| 252_M | 255_S | 1.039 | 0.75 |
| 47_L | 231_L | 1.034 | 0.74 |
| 175_R | 197_D | 1.033 | 0.74 |
| 53_P | 235_Y | 1.033 | 0.74 |
| 128_M | 232_K | 1.032 | 0.74 |
| 273_G | 309_V | 1.029 | 0.74 |
| 154_L | 164_E | 1.025 | 0.74 |
| 36_V | 225_N | 1.024 | 0.73 |
| 40_Y | 224_I | 1.019 | 0.73 |
| 151_N | 155_L | 1.011 | 0.72 |
| 24_I | 247_E | 1.011 | 0.72 |
| 261_L | 312_F | 1.010 | 0.72 |
| 238_N | 255_S | 1.008 | 0.72 |
| 274_E | 306_I | 1.006 | 0.72 |
| 47_L | 53_P | 1.006 | 0.72 |
| 27_K | 247_E | 1.005 | 0.71 |
| 337_G | 340_S | 1.003 | 0.71 |
| 16_L | 185_F | 1.002 | 0.71 |
| 10_L | 157_L | 1.002 | 0.71 |
| 221_D | 255_S | 1.001 | 0.71 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4il3A | 2 | 0.8261 | 99.8 | 0.744 | Contact Map |
| 4aw6A | 4 | 0.8087 | 99.6 | 0.776 | Contact Map |
| 3cqbA | 2 | 0.2957 | 98.8 | 0.852 | Contact Map |
| 3c37A | 2 | 0.571 | 98.3 | 0.87 | Contact Map |
| 4jixA | 2 | 0.3101 | 89.9 | 0.931 | Contact Map |
| 4jiuA | 1 | 0.2928 | 83.1 | 0.937 | Contact Map |
| 4qhjA | 2 | 0.2899 | 80.1 | 0.939 | Contact Map |
| 3tduC | 2 | 0.2087 | 8.3 | 0.966 | Contact Map |
| 3swyA | 3 | 0.1333 | 5.4 | 0.969 | Contact Map |
| 2kv5A | 1 | 0.0957 | 4.9 | 0.97 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)