| BZW2 -force run |
| ID: | 1455766409 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 419 (418) | ||
| Sequences: | 156 (89.4) | ||
| Seq/Len: | 0.373 | ||
| Nf(neff/√len): | 4.4 |
HHblits Results: (2015_06)
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: 0.373).
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 |
| 386_H | 391_K | 3.076 | 0.99 |
| 396_D | 399_K | 2.198 | 0.87 |
| 108_I | 154_L | 1.867 | 0.72 |
| 188_V | 233_Y | 1.829 | 0.70 |
| 244_D | 290_E | 1.822 | 0.69 |
| 187_A | 219_L | 1.775 | 0.67 |
| 98_V | 219_L | 1.742 | 0.64 |
| 308_N | 320_K | 1.713 | 0.63 |
| 216_L | 318_A | 1.678 | 0.60 |
| 345_K | 379_L | 1.677 | 0.60 |
| 160_G | 197_E | 1.637 | 0.57 |
| 413_E | 417_E | 1.569 | 0.53 |
| 6_K | 9_L | 1.558 | 0.52 |
| 46_E | 206_S | 1.508 | 0.48 |
| 7_P | 15_K | 1.502 | 0.48 |
| 156_G | 183_A | 1.494 | 0.47 |
| 401_F | 404_W | 1.484 | 0.46 |
| 343_L | 364_V | 1.481 | 0.46 |
| 16_T | 20_D | 1.468 | 0.45 |
| 302_M | 322_L | 1.452 | 0.44 |
| 152_A | 186_F | 1.452 | 0.44 |
| 152_A | 155_S | 1.446 | 0.44 |
| 17_R | 27_P | 1.430 | 0.43 |
| 1_M | 184_A | 1.422 | 0.42 |
| 65_A | 243_S | 1.419 | 0.42 |
| 188_V | 280_K | 1.417 | 0.42 |
| 117_K | 150_K | 1.413 | 0.41 |
| 222_V | 294_I | 1.391 | 0.40 |
| 145_E | 269_E | 1.386 | 0.40 |
| 274_E | 279_V | 1.386 | 0.40 |
| 305_V | 322_L | 1.384 | 0.39 |
| 5_Q | 410_E | 1.382 | 0.39 |
| 7_P | 11_G | 1.374 | 0.39 |
| 222_V | 292_A | 1.373 | 0.39 |
| 210_A | 219_L | 1.373 | 0.39 |
| 7_P | 18_K | 1.371 | 0.39 |
| 334_S | 339_E | 1.364 | 0.38 |
| 103_E | 146_T | 1.358 | 0.38 |
| 159_L | 190_L | 1.357 | 0.38 |
| 404_W | 408_A | 1.348 | 0.37 |
| 261_E | 278_Y | 1.325 | 0.36 |
| 297_L | 332_F | 1.315 | 0.35 |
| 61_Y | 97_C | 1.303 | 0.34 |
| 127_K | 216_L | 1.302 | 0.34 |
| 6_K | 11_G | 1.301 | 0.34 |
| 301_I | 329_L | 1.298 | 0.34 |
| 170_T | 276_V | 1.297 | 0.34 |
| 9_L | 18_K | 1.294 | 0.34 |
| 368_Y | 381_W | 1.291 | 0.33 |
| 186_F | 372_V | 1.291 | 0.33 |
| 133_M | 175_D | 1.280 | 0.33 |
| 137_L | 357_M | 1.275 | 0.32 |
| 244_D | 288_L | 1.274 | 0.32 |
| 220_F | 234_F | 1.272 | 0.32 |
| 34_L | 379_L | 1.262 | 0.32 |
| 43_D | 416_G | 1.257 | 0.31 |
| 177_L | 191_F | 1.249 | 0.31 |
| 175_D | 195_M | 1.239 | 0.30 |
| 8_V | 16_T | 1.239 | 0.30 |
| 391_K | 398_M | 1.237 | 0.30 |
| 189_K | 193_A | 1.234 | 0.30 |
| 18_K | 64_Y | 1.230 | 0.30 |
| 394_F | 405_L | 1.229 | 0.30 |
| 62_R | 362_K | 1.225 | 0.29 |
| 225_Q | 353_N | 1.222 | 0.29 |
| 16_T | 21_E | 1.221 | 0.29 |
| 302_M | 307_W | 1.215 | 0.29 |
| 66_D | 166_A | 1.215 | 0.29 |
| 11_G | 18_K | 1.213 | 0.29 |
| 17_R | 30_F | 1.211 | 0.28 |
| 148_Q | 249_Q | 1.207 | 0.28 |
| 151_L | 329_L | 1.205 | 0.28 |
| 19_R | 26_E | 1.204 | 0.28 |
| 398_M | 404_W | 1.202 | 0.28 |
| 99_F | 151_L | 1.201 | 0.28 |
| 18_K | 27_P | 1.195 | 0.28 |
| 345_K | 382_Y | 1.194 | 0.28 |
| 16_T | 19_R | 1.194 | 0.28 |
| 99_F | 197_E | 1.191 | 0.27 |
| 305_V | 329_L | 1.184 | 0.27 |
| 267_S | 346_V | 1.184 | 0.27 |
| 368_Y | 378_I | 1.182 | 0.27 |
| 288_L | 416_G | 1.181 | 0.27 |
| 199_D | 258_L | 1.176 | 0.26 |
| 9_L | 17_R | 1.176 | 0.26 |
| 378_I | 381_W | 1.175 | 0.26 |
| 226_S | 244_D | 1.173 | 0.26 |
| 136_L | 156_G | 1.172 | 0.26 |
| 254_T | 357_M | 1.171 | 0.26 |
| 305_V | 319_L | 1.167 | 0.26 |
| 291_T | 346_V | 1.166 | 0.26 |
| 187_A | 191_F | 1.165 | 0.26 |
| 353_N | 396_D | 1.165 | 0.26 |
| 156_G | 208_R | 1.163 | 0.26 |
| 284_K | 334_S | 1.162 | 0.26 |
| 190_L | 413_E | 1.159 | 0.26 |
| 60_D | 63_R | 1.156 | 0.25 |
| 141_K | 412_S | 1.155 | 0.25 |
| 108_I | 115_F | 1.155 | 0.25 |
| 100_S | 208_R | 1.154 | 0.25 |
| 243_S | 364_V | 1.153 | 0.25 |
| 78_L | 209_K | 1.152 | 0.25 |
| 284_K | 373_L | 1.152 | 0.25 |
| 93_M | 181_G | 1.151 | 0.25 |
| 171_S | 182_I | 1.148 | 0.25 |
| 375_E | 404_W | 1.148 | 0.25 |
| 42_G | 320_K | 1.145 | 0.25 |
| 144_S | 415_E | 1.144 | 0.25 |
| 372_V | 417_E | 1.143 | 0.25 |
| 266_L | 349_Y | 1.142 | 0.25 |
| 167_T | 274_E | 1.142 | 0.25 |
| 238_G | 352_D | 1.141 | 0.25 |
| 64_Y | 69_F | 1.139 | 0.24 |
| 43_D | 334_S | 1.137 | 0.24 |
| 143_F | 328_L | 1.137 | 0.24 |
| 127_K | 165_P | 1.126 | 0.24 |
| 313_L | 333_S | 1.125 | 0.24 |
| 16_T | 46_E | 1.125 | 0.24 |
| 402_V | 405_L | 1.124 | 0.24 |
| 164_L | 244_D | 1.123 | 0.24 |
| 232_K | 236_D | 1.122 | 0.24 |
| 99_F | 400_K | 1.120 | 0.23 |
| 93_M | 115_F | 1.120 | 0.23 |
| 60_D | 362_K | 1.119 | 0.23 |
| 132_E | 186_F | 1.119 | 0.23 |
| 128_A | 213_D | 1.118 | 0.23 |
| 116_N | 193_A | 1.116 | 0.23 |
| 67_T | 284_K | 1.115 | 0.23 |
| 110_N | 406_Q | 1.114 | 0.23 |
| 15_K | 18_K | 1.111 | 0.23 |
| 28_T | 279_V | 1.111 | 0.23 |
| 249_Q | 320_K | 1.111 | 0.23 |
| 34_L | 330_A | 1.110 | 0.23 |
| 290_E | 301_I | 1.108 | 0.23 |
| 24_K | 31_R | 1.106 | 0.23 |
| 27_P | 30_F | 1.105 | 0.23 |
| 26_E | 63_R | 1.105 | 0.23 |
| 226_S | 399_K | 1.104 | 0.23 |
| 11_G | 15_K | 1.103 | 0.23 |
| 63_R | 135_K | 1.102 | 0.23 |
| 177_L | 224_R | 1.102 | 0.23 |
| 195_M | 199_D | 1.101 | 0.23 |
| 8_V | 46_E | 1.101 | 0.23 |
| 26_E | 408_A | 1.100 | 0.22 |
| 5_Q | 26_E | 1.100 | 0.22 |
| 69_F | 130_E | 1.098 | 0.22 |
| 397_Q | 404_W | 1.098 | 0.22 |
| 290_E | 329_L | 1.094 | 0.22 |
| 219_L | 283_M | 1.094 | 0.22 |
| 103_E | 346_V | 1.091 | 0.22 |
| 180_E | 284_K | 1.091 | 0.22 |
| 20_D | 62_R | 1.091 | 0.22 |
| 85_I | 413_E | 1.090 | 0.22 |
| 68_L | 125_L | 1.088 | 0.22 |
| 18_K | 30_F | 1.084 | 0.22 |
| 157_I | 203_V | 1.083 | 0.22 |
| 147_E | 162_G | 1.078 | 0.21 |
| 266_L | 273_K | 1.077 | 0.21 |
| 5_Q | 189_K | 1.077 | 0.21 |
| 11_G | 17_R | 1.074 | 0.21 |
| 220_F | 233_Y | 1.073 | 0.21 |
| 98_V | 406_Q | 1.072 | 0.21 |
| 242_L | 414_S | 1.070 | 0.21 |
| 397_Q | 400_K | 1.069 | 0.21 |
| 119_I | 182_I | 1.069 | 0.21 |
| 284_K | 414_S | 1.067 | 0.21 |
| 19_R | 410_E | 1.066 | 0.21 |
| 7_P | 17_R | 1.064 | 0.21 |
| 351_Y | 390_G | 1.062 | 0.21 |
| 35_V | 43_D | 1.057 | 0.20 |
| 205_S | 346_V | 1.057 | 0.20 |
| 115_F | 181_G | 1.056 | 0.20 |
| 66_D | 175_D | 1.055 | 0.20 |
| 34_L | 343_L | 1.052 | 0.20 |
| 244_D | 352_D | 1.051 | 0.20 |
| 61_Y | 322_L | 1.050 | 0.20 |
| 48_V | 160_G | 1.050 | 0.20 |
| 91_T | 104_D | 1.048 | 0.20 |
| 207_L | 225_Q | 1.045 | 0.20 |
| 9_L | 15_K | 1.044 | 0.20 |
| 80_P | 117_K | 1.042 | 0.20 |
| 50_K | 288_L | 1.041 | 0.20 |
| 88_G | 209_K | 1.040 | 0.20 |
| 71_I | 142_A | 1.038 | 0.20 |
| 412_S | 416_G | 1.038 | 0.20 |
| 234_F | 371_D | 1.037 | 0.20 |
| 398_M | 401_F | 1.035 | 0.19 |
| 73_V | 133_M | 1.034 | 0.19 |
| 17_R | 64_Y | 1.031 | 0.19 |
| 72_L | 97_C | 1.031 | 0.19 |
| 266_L | 271_P | 1.030 | 0.19 |
| 116_N | 156_G | 1.029 | 0.19 |
| 349_Y | 417_E | 1.029 | 0.19 |
| 212_L | 301_I | 1.029 | 0.19 |
| 2_N | 66_D | 1.029 | 0.19 |
| 358_K | 390_G | 1.029 | 0.19 |
| 409_E | 414_S | 1.028 | 0.19 |
| 11_G | 59_L | 1.028 | 0.19 |
| 108_I | 165_P | 1.027 | 0.19 |
| 332_F | 339_E | 1.026 | 0.19 |
| 56_G | 68_L | 1.025 | 0.19 |
| 168_I | 320_K | 1.024 | 0.19 |
| 65_A | 250_Q | 1.022 | 0.19 |
| 288_L | 339_E | 1.022 | 0.19 |
| 14_F | 406_Q | 1.020 | 0.19 |
| 13_R | 382_Y | 1.020 | 0.19 |
| 122_Y | 179_K | 1.020 | 0.19 |
| 323_K | 334_S | 1.020 | 0.19 |
| 22_K | 52_L | 1.019 | 0.19 |
| 260_K | 413_E | 1.019 | 0.19 |
| 98_V | 187_A | 1.018 | 0.19 |
| 336_G | 339_E | 1.016 | 0.19 |
| 330_A | 349_Y | 1.016 | 0.19 |
| 52_L | 68_L | 1.014 | 0.18 |
| 262_L | 298_W | 1.012 | 0.18 |
| 108_I | 331_V | 1.012 | 0.18 |
| 72_L | 374_S | 1.011 | 0.18 |
| 407_N | 412_S | 1.011 | 0.18 |
| 98_V | 270_C | 1.010 | 0.18 |
| 262_L | 319_L | 1.010 | 0.18 |
| 239_L | 328_L | 1.009 | 0.18 |
| 208_R | 249_Q | 1.006 | 0.18 |
| 46_E | 330_A | 1.004 | 0.18 |
| 113_Q | 127_K | 1.003 | 0.18 |
| 364_V | 375_E | 1.002 | 0.18 |
| 112_A | 119_I | 1.002 | 0.18 |
| 290_E | 338_S | 1.001 | 0.18 |
| 290_E | 352_D | 1.000 | 0.18 |
| 10_T | 314_V | 1.000 | 0.18 |
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 | |
| 3l6aA | 1 | 0.8019 | 100 | 0.772 | Contact Map |
| 1ug3A | 2 | 0.7589 | 100 | 0.781 | Contact Map |
| 3juiA | 1 | 0.401 | 100 | 0.808 | Contact Map |
| 1paqA | 1 | 0.3747 | 100 | 0.813 | Contact Map |
| 2fulA | 6 | 0.3819 | 100 | 0.822 | Contact Map |
| 3d3mA | 2 | 0.3508 | 100 | 0.83 | Contact Map |
| 2iu1A | 1 | 0.3771 | 100 | 0.842 | Contact Map |
| 1h2vC | 1 | 0.7924 | 97.9 | 0.95 | Contact Map |
| 3opbA | 2 | 0.8234 | 62.3 | 0.977 | Contact Map |
| 2nvmA | 2 | 0.2458 | 27.3 | 0.982 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)