| T0808 -force run |
| ID: | 1402092408 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 418 (411) | ||
| Sequences: | 81 (70.6) | ||
| Seq/Len: | 0.197 | ||
| Nf(neff/√len): | 3.5 |
Jackhmmer Results: (2014_04_16)
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: 0.197).
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 |
| 61_F | 117_I | 2.246 | 0.74 |
| 215_L | 258_Q | 2.055 | 0.64 |
| 174_W | 290_Y | 1.987 | 0.60 |
| 353_T | 401_C | 1.919 | 0.56 |
| 351_R | 401_C | 1.918 | 0.56 |
| 190_S | 245_V | 1.912 | 0.56 |
| 220_S | 255_S | 1.897 | 0.55 |
| 25_V | 57_V | 1.811 | 0.50 |
| 174_W | 316_R | 1.797 | 0.49 |
| 226_N | 229_E | 1.790 | 0.48 |
| 363_A | 371_Y | 1.740 | 0.45 |
| 277_I | 314_Y | 1.738 | 0.45 |
| 239_L | 305_F | 1.682 | 0.42 |
| 175_F | 317_P | 1.670 | 0.41 |
| 173_E | 276_Q | 1.638 | 0.39 |
| 275_M | 289_A | 1.636 | 0.39 |
| 252_N | 301_L | 1.627 | 0.39 |
| 34_T | 283_G | 1.603 | 0.37 |
| 248_G | 252_N | 1.587 | 0.36 |
| 220_S | 227_P | 1.568 | 0.35 |
| 94_L | 382_Y | 1.542 | 0.34 |
| 163_L | 335_V | 1.540 | 0.34 |
| 220_S | 230_I | 1.513 | 0.32 |
| 305_F | 367_V | 1.470 | 0.30 |
| 261_L | 302_I | 1.470 | 0.30 |
| 283_G | 383_L | 1.445 | 0.29 |
| 119_L | 300_K | 1.444 | 0.29 |
| 269_N | 293_A | 1.443 | 0.29 |
| 362_T | 399_F | 1.424 | 0.28 |
| 290_Y | 352_L | 1.422 | 0.28 |
| 189_H | 385_M | 1.400 | 0.27 |
| 154_W | 236_I | 1.393 | 0.26 |
| 186_E | 385_M | 1.372 | 0.25 |
| 34_T | 58_S | 1.352 | 0.25 |
| 67_T | 139_N | 1.348 | 0.24 |
| 186_E | 206_Y | 1.347 | 0.24 |
| 309_K | 386_G | 1.345 | 0.24 |
| 174_W | 352_L | 1.342 | 0.24 |
| 227_P | 255_S | 1.341 | 0.24 |
| 290_Y | 317_P | 1.333 | 0.24 |
| 230_I | 255_S | 1.326 | 0.23 |
| 165_Y | 177_N | 1.325 | 0.23 |
| 359_H | 395_M | 1.322 | 0.23 |
| 199_E | 312_T | 1.321 | 0.23 |
| 62_Y | 132_I | 1.319 | 0.23 |
| 25_V | 173_E | 1.314 | 0.23 |
| 220_S | 224_T | 1.308 | 0.23 |
| 204_M | 214_I | 1.306 | 0.23 |
| 158_G | 373_G | 1.293 | 0.22 |
| 158_G | 307_R | 1.292 | 0.22 |
| 353_T | 405_G | 1.283 | 0.22 |
| 155_G | 220_S | 1.277 | 0.21 |
| 328_Q | 386_G | 1.276 | 0.21 |
| 175_F | 290_Y | 1.274 | 0.21 |
| 186_E | 189_H | 1.265 | 0.21 |
| 157_R | 307_R | 1.259 | 0.21 |
| 249_E | 287_Y | 1.253 | 0.20 |
| 238_L | 294_T | 1.251 | 0.20 |
| 158_G | 221_P | 1.250 | 0.20 |
| 337_F | 383_L | 1.242 | 0.20 |
| 154_W | 372_Q | 1.238 | 0.20 |
| 43_T | 81_I | 1.238 | 0.20 |
| 146_Y | 318_H | 1.228 | 0.19 |
| 206_Y | 314_Y | 1.228 | 0.19 |
| 213_R | 304_S | 1.226 | 0.19 |
| 109_I | 344_S | 1.225 | 0.19 |
| 63_L | 117_I | 1.219 | 0.19 |
| 314_Y | 317_P | 1.218 | 0.19 |
| 121_G | 129_F | 1.217 | 0.19 |
| 58_S | 118_D | 1.208 | 0.19 |
| 277_I | 284_N | 1.208 | 0.19 |
| 32_Y | 275_M | 1.207 | 0.19 |
| 30_N | 389_F | 1.205 | 0.19 |
| 147_V | 155_G | 1.198 | 0.18 |
| 77_G | 397_T | 1.197 | 0.18 |
| 337_F | 344_S | 1.195 | 0.18 |
| 224_T | 255_S | 1.195 | 0.18 |
| 157_R | 373_G | 1.194 | 0.18 |
| 255_S | 301_L | 1.192 | 0.18 |
| 288_T | 305_F | 1.188 | 0.18 |
| 194_A | 273_F | 1.178 | 0.18 |
| 157_R | 389_F | 1.175 | 0.18 |
| 215_L | 415_L | 1.173 | 0.17 |
| 189_H | 225_Q | 1.172 | 0.17 |
| 84_S | 382_Y | 1.171 | 0.17 |
| 158_G | 389_F | 1.167 | 0.17 |
| 92_V | 260_Y | 1.166 | 0.17 |
| 180_T | 270_T | 1.165 | 0.17 |
| 28_S | 290_Y | 1.164 | 0.17 |
| 271_Y | 310_T | 1.161 | 0.17 |
| 47_V | 393_V | 1.158 | 0.17 |
| 155_G | 363_A | 1.150 | 0.17 |
| 275_M | 314_Y | 1.149 | 0.17 |
| 155_G | 305_F | 1.148 | 0.17 |
| 261_L | 326_P | 1.147 | 0.17 |
| 33_V | 214_I | 1.147 | 0.17 |
| 258_Q | 415_L | 1.147 | 0.17 |
| 119_L | 222_F | 1.147 | 0.17 |
| 208_S | 388_F | 1.145 | 0.17 |
| 307_R | 373_G | 1.143 | 0.16 |
| 340_Q | 355_A | 1.142 | 0.16 |
| 187_T | 386_G | 1.140 | 0.16 |
| 109_I | 204_M | 1.139 | 0.16 |
| 47_V | 318_H | 1.138 | 0.16 |
| 220_S | 301_L | 1.137 | 0.16 |
| 215_L | 260_Y | 1.135 | 0.16 |
| 249_E | 252_N | 1.134 | 0.16 |
| 32_Y | 328_Q | 1.134 | 0.16 |
| 221_P | 307_R | 1.133 | 0.16 |
| 231_P | 252_N | 1.132 | 0.16 |
| 149_D | 393_V | 1.128 | 0.16 |
| 47_V | 375_N | 1.128 | 0.16 |
| 176_Y | 272_K | 1.123 | 0.16 |
| 252_N | 255_S | 1.122 | 0.16 |
| 157_R | 221_P | 1.119 | 0.16 |
| 231_P | 255_S | 1.118 | 0.16 |
| 84_S | 143_K | 1.114 | 0.15 |
| 52_N | 382_Y | 1.113 | 0.15 |
| 313_W | 362_T | 1.112 | 0.15 |
| 204_M | 232_D | 1.111 | 0.15 |
| 247_I | 315_K | 1.108 | 0.15 |
| 61_F | 137_A | 1.107 | 0.15 |
| 342_A | 406_K | 1.102 | 0.15 |
| 58_S | 120_Q | 1.101 | 0.15 |
| 32_Y | 139_N | 1.100 | 0.15 |
| 30_N | 157_R | 1.100 | 0.15 |
| 221_P | 257_G | 1.098 | 0.15 |
| 153_Y | 310_T | 1.096 | 0.15 |
| 167_L | 383_L | 1.096 | 0.15 |
| 94_L | 185_G | 1.095 | 0.15 |
| 149_D | 152_D | 1.094 | 0.15 |
| 204_M | 337_F | 1.092 | 0.15 |
| 236_I | 248_G | 1.090 | 0.15 |
| 155_G | 255_S | 1.088 | 0.15 |
| 190_S | 236_I | 1.087 | 0.15 |
| 34_T | 383_L | 1.087 | 0.15 |
| 236_I | 249_E | 1.085 | 0.15 |
| 227_P | 252_N | 1.084 | 0.15 |
| 184_E | 192_Y | 1.084 | 0.15 |
| 326_P | 383_L | 1.084 | 0.15 |
| 283_G | 412_W | 1.081 | 0.14 |
| 277_I | 313_W | 1.081 | 0.14 |
| 261_L | 378_D | 1.079 | 0.14 |
| 318_H | 412_W | 1.079 | 0.14 |
| 25_V | 82_K | 1.076 | 0.14 |
| 236_I | 252_N | 1.074 | 0.14 |
| 199_E | 222_F | 1.073 | 0.14 |
| 207_N | 213_R | 1.072 | 0.14 |
| 159_P | 258_Q | 1.071 | 0.14 |
| 307_R | 389_F | 1.071 | 0.14 |
| 359_H | 372_Q | 1.069 | 0.14 |
| 30_N | 158_G | 1.069 | 0.14 |
| 231_P | 415_L | 1.067 | 0.14 |
| 290_Y | 316_R | 1.067 | 0.14 |
| 155_G | 230_I | 1.067 | 0.14 |
| 206_Y | 385_M | 1.066 | 0.14 |
| 159_P | 215_L | 1.066 | 0.14 |
| 78_H | 179_I | 1.065 | 0.14 |
| 146_Y | 315_K | 1.065 | 0.14 |
| 20_P | 117_I | 1.064 | 0.14 |
| 221_P | 373_G | 1.063 | 0.14 |
| 117_I | 152_D | 1.063 | 0.14 |
| 32_Y | 386_G | 1.062 | 0.14 |
| 373_G | 389_F | 1.061 | 0.14 |
| 195_A | 415_L | 1.060 | 0.14 |
| 44_Q | 292_Y | 1.060 | 0.14 |
| 150_F | 367_V | 1.058 | 0.14 |
| 90_F | 107_I | 1.057 | 0.14 |
| 259_S | 355_A | 1.056 | 0.14 |
| 290_Y | 416_K | 1.054 | 0.14 |
| 192_Y | 342_A | 1.054 | 0.14 |
| 122_V | 188_M | 1.053 | 0.14 |
| 239_L | 316_R | 1.053 | 0.14 |
| 66_P | 337_F | 1.053 | 0.14 |
| 84_S | 337_F | 1.051 | 0.14 |
| 26_G | 342_A | 1.050 | 0.14 |
| 32_Y | 313_W | 1.050 | 0.14 |
| 227_P | 230_I | 1.049 | 0.14 |
| 94_L | 209_P | 1.049 | 0.14 |
| 67_T | 210_T | 1.046 | 0.13 |
| 317_P | 335_V | 1.045 | 0.13 |
| 69_A | 146_Y | 1.045 | 0.13 |
| 46_G | 212_R | 1.039 | 0.13 |
| 298_E | 313_W | 1.037 | 0.13 |
| 372_Q | 416_K | 1.036 | 0.13 |
| 362_T | 388_F | 1.035 | 0.13 |
| 155_G | 321_L | 1.034 | 0.13 |
| 220_S | 307_R | 1.033 | 0.13 |
| 52_N | 60_Y | 1.033 | 0.13 |
| 341_W | 353_T | 1.032 | 0.13 |
| 173_E | 278_R | 1.032 | 0.13 |
| 25_V | 102_V | 1.030 | 0.13 |
| 75_A | 94_L | 1.028 | 0.13 |
| 271_Y | 373_G | 1.028 | 0.13 |
| 30_N | 220_S | 1.028 | 0.13 |
| 213_R | 252_N | 1.026 | 0.13 |
| 195_A | 215_L | 1.025 | 0.13 |
| 109_I | 407_E | 1.024 | 0.13 |
| 210_T | 235_K | 1.024 | 0.13 |
| 56_I | 120_Q | 1.022 | 0.13 |
| 220_S | 231_P | 1.021 | 0.13 |
| 337_F | 392_S | 1.021 | 0.13 |
| 227_P | 301_L | 1.020 | 0.13 |
| 58_S | 116_R | 1.020 | 0.13 |
| 277_I | 317_P | 1.019 | 0.13 |
| 383_L | 399_F | 1.018 | 0.13 |
| 271_Y | 291_F | 1.017 | 0.13 |
| 220_S | 252_N | 1.016 | 0.13 |
| 225_Q | 315_K | 1.016 | 0.13 |
| 211_E | 308_P | 1.016 | 0.13 |
| 174_W | 317_P | 1.013 | 0.13 |
| 288_T | 312_T | 1.013 | 0.13 |
| 324_F | 388_F | 1.012 | 0.13 |
| 69_A | 139_N | 1.012 | 0.13 |
| 105_G | 303_A | 1.012 | 0.13 |
| 213_R | 255_S | 1.012 | 0.13 |
| 31_G | 135_L | 1.011 | 0.13 |
| 232_D | 409_E | 1.010 | 0.12 |
| 288_T | 301_L | 1.010 | 0.12 |
| 337_F | 356_T | 1.010 | 0.12 |
| 182_P | 289_A | 1.010 | 0.12 |
| 202_F | 212_R | 1.010 | 0.12 |
| 155_G | 207_N | 1.009 | 0.12 |
| 327_E | 399_F | 1.008 | 0.12 |
| 193_M | 215_L | 1.008 | 0.12 |
| 159_P | 182_P | 1.008 | 0.12 |
| 292_Y | 366_Q | 1.007 | 0.12 |
| 231_P | 305_F | 1.007 | 0.12 |
| 53_P | 209_P | 1.007 | 0.12 |
| 155_G | 221_P | 1.006 | 0.12 |
| 233_D | 236_I | 1.006 | 0.12 |
| 202_F | 355_A | 1.005 | 0.12 |
| 221_P | 255_S | 1.004 | 0.12 |
| 344_S | 350_S | 1.003 | 0.12 |
| 154_W | 168_P | 1.001 | 0.12 |
| 189_H | 192_Y | 1.000 | 0.12 |
| 218_V | 302_I | 1.000 | 0.12 |
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 | |
| 2bgoA | 1 | 0.2679 | 93.5 | 0.968 | Contact Map |
| 4kmqA | 1 | 0.3014 | 82.5 | 0.974 | Contact Map |
| 2w87A | 2 | 0.3038 | 79.3 | 0.975 | Contact Map |
| 2vzpA | 2 | 0.2775 | 74.9 | 0.976 | Contact Map |
| 2vzsA | 2 | 0.0598 | 71.3 | 0.977 | Contact Map |
| 2w47A | 1 | 0.2967 | 64.2 | 0.978 | Contact Map |
| 2wz8A | 1 | 0.2703 | 63.8 | 0.978 | Contact Map |
| 2w3jA | 1 | 0.3038 | 59.4 | 0.978 | Contact Map |
| 2y8kA | 1 | 0.3206 | 37.1 | 0.981 | Contact Map |
| 2xwxA | 2 | 0.323 | 34.7 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)