| T0814 -force run |
| ID: | 1404849462 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 424 (412) | ||
| Sequences: | 232 (210.3) | ||
| Seq/Len: | 0.563 | ||
| Nf(neff/√len): | 10.4 |
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: 0.563).
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 |
| 348_N | 355_E | 6.011 | 1.00 |
| 82_N | 86_T | 4.004 | 1.00 |
| 160_E | 410_R | 3.677 | 1.00 |
| 277_D | 369_Y | 3.079 | 1.00 |
| 402_R | 409_D | 2.794 | 0.99 |
| 167_A | 397_I | 2.679 | 0.98 |
| 134_S | 160_E | 2.543 | 0.98 |
| 186_F | 397_I | 2.425 | 0.97 |
| 290_D | 392_Q | 2.196 | 0.93 |
| 74_Y | 151_I | 2.072 | 0.90 |
| 327_S | 344_K | 2.059 | 0.90 |
| 345_M | 356_K | 2.042 | 0.89 |
| 396_S | 414_V | 1.911 | 0.85 |
| 157_S | 411_L | 1.903 | 0.84 |
| 195_I | 202_L | 1.884 | 0.84 |
| 66_G | 74_Y | 1.860 | 0.82 |
| 141_V | 152_F | 1.811 | 0.80 |
| 82_N | 408_Y | 1.792 | 0.79 |
| 211_R | 214_N | 1.728 | 0.76 |
| 271_N | 315_H | 1.706 | 0.74 |
| 80_H | 88_S | 1.703 | 0.74 |
| 398_Y | 411_L | 1.698 | 0.74 |
| 340_D | 343_S | 1.682 | 0.73 |
| 40_V | 154_A | 1.677 | 0.72 |
| 40_V | 60_I | 1.650 | 0.71 |
| 329_Y | 343_S | 1.643 | 0.70 |
| 244_E | 392_Q | 1.635 | 0.70 |
| 40_V | 62_I | 1.622 | 0.69 |
| 260_V | 274_L | 1.618 | 0.68 |
| 112_G | 345_M | 1.606 | 0.68 |
| 244_E | 292_D | 1.600 | 0.67 |
| 403_P | 406_A | 1.569 | 0.65 |
| 163_V | 193_F | 1.556 | 0.64 |
| 88_S | 198_P | 1.552 | 0.64 |
| 157_S | 398_Y | 1.550 | 0.64 |
| 151_I | 165_I | 1.547 | 0.63 |
| 219_L | 237_L | 1.505 | 0.60 |
| 244_E | 290_D | 1.479 | 0.58 |
| 203_K | 402_R | 1.450 | 0.56 |
| 94_E | 407_R | 1.449 | 0.56 |
| 297_I | 326_G | 1.423 | 0.54 |
| 202_L | 229_I | 1.421 | 0.54 |
| 202_L | 399_V | 1.419 | 0.54 |
| 62_I | 154_A | 1.415 | 0.53 |
| 245_Y | 344_K | 1.414 | 0.53 |
| 165_I | 399_V | 1.398 | 0.52 |
| 253_N | 312_Y | 1.389 | 0.51 |
| 133_V | 310_D | 1.357 | 0.49 |
| 92_P | 100_Q | 1.344 | 0.48 |
| 182_Q | 393_N | 1.334 | 0.47 |
| 280_R | 385_E | 1.328 | 0.46 |
| 276_T | 317_T | 1.320 | 0.46 |
| 176_D | 181_H | 1.320 | 0.46 |
| 207_Y | 212_R | 1.319 | 0.46 |
| 335_F | 343_S | 1.317 | 0.45 |
| 134_S | 184_V | 1.305 | 0.45 |
| 52_I | 60_I | 1.302 | 0.44 |
| 63_N | 306_D | 1.298 | 0.44 |
| 241_A | 389_Y | 1.292 | 0.43 |
| 11_M | 51_Y | 1.290 | 0.43 |
| 153_T | 236_N | 1.272 | 0.42 |
| 292_D | 392_Q | 1.271 | 0.42 |
| 329_Y | 344_K | 1.267 | 0.42 |
| 14_F | 19_G | 1.260 | 0.41 |
| 250_F | 312_Y | 1.258 | 0.41 |
| 207_Y | 398_Y | 1.257 | 0.41 |
| 78_V | 180_S | 1.241 | 0.40 |
| 79_V | 140_Q | 1.241 | 0.40 |
| 23_Q | 330_L | 1.234 | 0.39 |
| 106_D | 121_R | 1.225 | 0.38 |
| 35_I | 344_K | 1.222 | 0.38 |
| 76_Y | 126_N | 1.209 | 0.37 |
| 206_V | 347_Y | 1.208 | 0.37 |
| 122_L | 139_I | 1.208 | 0.37 |
| 360_L | 365_Y | 1.204 | 0.37 |
| 270_Y | 389_Y | 1.202 | 0.37 |
| 95_Y | 158_V | 1.201 | 0.37 |
| 82_N | 409_D | 1.196 | 0.36 |
| 213_D | 399_V | 1.189 | 0.36 |
| 171_G | 178_N | 1.186 | 0.35 |
| 195_I | 201_D | 1.185 | 0.35 |
| 12_M | 373_P | 1.183 | 0.35 |
| 127_D | 188_I | 1.183 | 0.35 |
| 299_C | 302_C | 1.181 | 0.35 |
| 141_V | 309_A | 1.181 | 0.35 |
| 76_Y | 98_G | 1.176 | 0.35 |
| 162_V | 241_A | 1.169 | 0.34 |
| 283_G | 317_T | 1.169 | 0.34 |
| 101_G | 133_V | 1.168 | 0.34 |
| 316_F | 360_L | 1.167 | 0.34 |
| 66_G | 139_I | 1.167 | 0.34 |
| 256_N | 260_V | 1.167 | 0.34 |
| 207_Y | 396_S | 1.166 | 0.34 |
| 131_F | 284_T | 1.165 | 0.34 |
| 93_I | 287_Y | 1.162 | 0.34 |
| 193_F | 401_Y | 1.158 | 0.33 |
| 74_Y | 152_F | 1.156 | 0.33 |
| 351_T | 355_E | 1.155 | 0.33 |
| 204_I | 301_D | 1.149 | 0.33 |
| 318_L | 384_I | 1.148 | 0.33 |
| 53_A | 330_L | 1.144 | 0.32 |
| 124_L | 131_F | 1.140 | 0.32 |
| 252_S | 310_D | 1.138 | 0.32 |
| 85_W | 136_N | 1.131 | 0.32 |
| 216_V | 260_V | 1.131 | 0.32 |
| 28_T | 31_N | 1.131 | 0.32 |
| 97_N | 130_Q | 1.131 | 0.32 |
| 166_S | 360_L | 1.130 | 0.31 |
| 38_L | 62_I | 1.130 | 0.31 |
| 9_L | 16_L | 1.129 | 0.31 |
| 330_L | 358_V | 1.129 | 0.31 |
| 246_R | 385_E | 1.126 | 0.31 |
| 176_D | 369_Y | 1.121 | 0.31 |
| 171_G | 251_L | 1.121 | 0.31 |
| 188_I | 413_G | 1.115 | 0.30 |
| 206_V | 237_L | 1.115 | 0.30 |
| 55_G | 166_S | 1.114 | 0.30 |
| 188_I | 399_V | 1.110 | 0.30 |
| 343_S | 358_V | 1.106 | 0.30 |
| 100_Q | 152_F | 1.103 | 0.30 |
| 37_T | 195_I | 1.101 | 0.30 |
| 54_L | 137_Y | 1.099 | 0.29 |
| 186_F | 204_I | 1.098 | 0.29 |
| 35_I | 74_Y | 1.096 | 0.29 |
| 165_I | 415_T | 1.092 | 0.29 |
| 77_N | 108_A | 1.091 | 0.29 |
| 183_Q | 238_I | 1.091 | 0.29 |
| 31_N | 152_F | 1.084 | 0.28 |
| 94_E | 309_A | 1.075 | 0.28 |
| 366_N | 403_P | 1.073 | 0.28 |
| 136_N | 400_Y | 1.068 | 0.27 |
| 213_D | 370_L | 1.066 | 0.27 |
| 13_L | 21_N | 1.065 | 0.27 |
| 98_G | 126_N | 1.064 | 0.27 |
| 196_T | 245_Y | 1.057 | 0.27 |
| 280_R | 369_Y | 1.057 | 0.27 |
| 90_L | 260_V | 1.055 | 0.27 |
| 247_R | 364_S | 1.053 | 0.26 |
| 86_T | 346_G | 1.053 | 0.26 |
| 86_T | 350_E | 1.050 | 0.26 |
| 51_Y | 132_K | 1.049 | 0.26 |
| 138_A | 278_Y | 1.048 | 0.26 |
| 188_I | 276_T | 1.048 | 0.26 |
| 28_T | 251_L | 1.048 | 0.26 |
| 66_G | 212_R | 1.048 | 0.26 |
| 8_L | 14_F | 1.048 | 0.26 |
| 131_F | 252_S | 1.047 | 0.26 |
| 117_Y | 213_D | 1.046 | 0.26 |
| 167_A | 186_F | 1.046 | 0.26 |
| 215_A | 401_Y | 1.045 | 0.26 |
| 313_I | 357_A | 1.041 | 0.26 |
| 184_V | 356_K | 1.040 | 0.26 |
| 141_V | 224_I | 1.040 | 0.26 |
| 403_P | 410_R | 1.039 | 0.26 |
| 245_Y | 337_N | 1.037 | 0.25 |
| 21_N | 345_M | 1.033 | 0.25 |
| 165_I | 397_I | 1.031 | 0.25 |
| 386_G | 393_N | 1.031 | 0.25 |
| 40_V | 249_E | 1.030 | 0.25 |
| 119_N | 341_E | 1.029 | 0.25 |
| 249_E | 288_D | 1.029 | 0.25 |
| 198_P | 203_K | 1.029 | 0.25 |
| 138_A | 206_V | 1.028 | 0.25 |
| 168_S | 185_S | 1.028 | 0.25 |
| 54_L | 367_Y | 1.027 | 0.25 |
| 362_Q | 409_D | 1.024 | 0.25 |
| 241_A | 350_E | 1.024 | 0.25 |
| 207_Y | 384_I | 1.023 | 0.25 |
| 102_T | 163_V | 1.017 | 0.24 |
| 89_Q | 403_P | 1.017 | 0.24 |
| 213_D | 375_G | 1.017 | 0.24 |
| 84_D | 190_N | 1.016 | 0.24 |
| 328_V | 358_V | 1.016 | 0.24 |
| 16_L | 132_K | 1.014 | 0.24 |
| 187_N | 262_N | 1.010 | 0.24 |
| 181_H | 240_P | 1.007 | 0.24 |
| 181_H | 387_N | 1.007 | 0.24 |
| 45_E | 220_Q | 1.007 | 0.24 |
| 107_F | 203_K | 1.007 | 0.24 |
| 251_L | 364_S | 1.004 | 0.24 |
| 183_Q | 246_R | 1.004 | 0.24 |
| 35_I | 66_G | 1.003 | 0.23 |
| 13_L | 89_Q | 1.003 | 0.23 |
| 121_R | 359_L | 1.001 | 0.23 |
| 8_L | 36_K | 1.001 | 0.23 |
| 315_H | 365_Y | 1.000 | 0.23 |
| 245_Y | 298_R | 1.000 | 0.23 |
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 | |
| 4r7fA | 1 | 0.9363 | 100 | 0.063 | Contact Map |
| 2qlvB | 2 | 0.2028 | 97 | 0.953 | Contact Map |
| 4aeeA | 2 | 0.2925 | 97 | 0.953 | Contact Map |
| 4aefA | 2 | 0.2807 | 96.4 | 0.956 | Contact Map |
| 1z0nA | 3 | 0.2028 | 96.3 | 0.957 | Contact Map |
| 2lu3A | 1 | 0.2453 | 95.5 | 0.959 | Contact Map |
| 1ac0A | 1 | 0.2382 | 94.4 | 0.962 | Contact Map |
| 4cfeB | 2 | 0.2241 | 93.9 | 0.963 | Contact Map |
| 2z0bA | 6 | 0.2547 | 90.5 | 0.966 | Contact Map |
| 4pyhA | 1 | 0.592 | 71.4 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)