| Mrn1 |
| ID: | 1441333925 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 426 (345) | ||
| Sequences: | 448 (345.2) | ||
| Seq/Len: | 1.299 | ||
| Nf(neff/√len): | 18.6 |
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: 1.299).
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 |
| 289_T | 299_Q | 2.619 | 1.00 |
| 358_Q | 368_E | 2.516 | 1.00 |
| 335_T | 345_D | 2.219 | 0.99 |
| 98_R | 119_D | 2.165 | 0.99 |
| 381_I | 391_K | 2.119 | 0.98 |
| 379_K | 393_D | 2.030 | 0.98 |
| 126_C | 137_E | 2.006 | 0.97 |
| 371_F | 417_F | 1.972 | 0.97 |
| 284_K | 305_G | 1.958 | 0.97 |
| 404_I | 414_E | 1.910 | 0.96 |
| 321_Y | 334_G | 1.880 | 0.96 |
| 390_Y | 403_G | 1.880 | 0.96 |
| 195_I | 209_Q | 1.812 | 0.94 |
| 395_E | 400_N | 1.812 | 0.94 |
| 168_K | 190_G | 1.752 | 0.93 |
| 256_F | 348_W | 1.734 | 0.93 |
| 197_K | 207_E | 1.721 | 0.92 |
| 264_H | 278_E | 1.695 | 0.91 |
| 367_Y | 380_G | 1.691 | 0.91 |
| 104_Y | 116_W | 1.677 | 0.91 |
| 148_F | 162_T | 1.649 | 0.90 |
| 326_K | 331_E | 1.636 | 0.89 |
| 358_Q | 366_A | 1.631 | 0.89 |
| 234_L | 239_H | 1.622 | 0.89 |
| 243_V | 253_E | 1.610 | 0.88 |
| 138_G | 149_G | 1.576 | 0.87 |
| 121_F | 143_G | 1.575 | 0.87 |
| 261_K | 282_D | 1.566 | 0.87 |
| 381_I | 389_Y | 1.562 | 0.86 |
| 173_V | 184_E | 1.554 | 0.86 |
| 348_W | 394_W | 1.546 | 0.86 |
| 333_L | 347_E | 1.523 | 0.84 |
| 310_P | 324_E | 1.507 | 0.84 |
| 292_F | 338_M | 1.499 | 0.83 |
| 183_Y | 196_G | 1.495 | 0.83 |
| 275_Y | 288_G | 1.494 | 0.83 |
| 346_G | 357_G | 1.493 | 0.83 |
| 156_G | 272_G | 1.492 | 0.83 |
| 307_R | 328_D | 1.479 | 0.82 |
| 400_N | 419_N | 1.462 | 0.81 |
| 402_K | 416_Y | 1.461 | 0.81 |
| 369_G | 380_G | 1.426 | 0.79 |
| 344_Y | 357_G | 1.422 | 0.78 |
| 345_D | 391_K | 1.404 | 0.77 |
| 125_R | 149_G | 1.391 | 0.76 |
| 163_W | 325_W | 1.386 | 0.76 |
| 219_G | 233_W | 1.378 | 0.75 |
| 356_K | 370_Y | 1.374 | 0.75 |
| 375_L | 396_Q | 1.374 | 0.75 |
| 241_Y | 255_N | 1.366 | 0.74 |
| 210_W | 325_W | 1.366 | 0.74 |
| 114_G | 125_R | 1.363 | 0.74 |
| 372_V | 377_Q | 1.343 | 0.73 |
| 114_G | 149_G | 1.334 | 0.72 |
| 185_G | 357_G | 1.333 | 0.72 |
| 220_I | 230_E | 1.316 | 0.70 |
| 103_I | 113_V | 1.314 | 0.70 |
| 89_Y | 102_G | 1.314 | 0.70 |
| 288_G | 300_G | 1.302 | 0.69 |
| 130_F | 246_C | 1.297 | 0.69 |
| 218_K | 232_D | 1.294 | 0.68 |
| 298_Y | 311_G | 1.293 | 0.68 |
| 171_Q | 186_E | 1.288 | 0.68 |
| 125_R | 138_G | 1.288 | 0.68 |
| 346_G | 369_G | 1.285 | 0.68 |
| 112_Y | 125_R | 1.284 | 0.68 |
| 124_Q | 139_Q | 1.279 | 0.67 |
| 102_G | 185_G | 1.266 | 0.66 |
| 185_G | 208_G | 1.266 | 0.66 |
| 155_N | 376_R | 1.265 | 0.66 |
| 93_L | 140_L | 1.263 | 0.66 |
| 172_G | 187_W | 1.260 | 0.65 |
| 159_Y | 172_G | 1.257 | 0.65 |
| 179_S | 190_G | 1.246 | 0.64 |
| 149_G | 172_G | 1.232 | 0.63 |
| 354_N | 372_V | 1.230 | 0.63 |
| 161_G | 300_G | 1.230 | 0.63 |
| 149_G | 231_G | 1.229 | 0.63 |
| 185_G | 346_G | 1.226 | 0.62 |
| 208_G | 219_G | 1.225 | 0.62 |
| 403_G | 415_G | 1.220 | 0.62 |
| 277_G | 346_G | 1.219 | 0.62 |
| 149_G | 185_G | 1.216 | 0.61 |
| 192_K | 210_W | 1.211 | 0.61 |
| 312_V | 322_D | 1.201 | 0.60 |
| 161_G | 357_G | 1.198 | 0.60 |
| 390_Y | 415_G | 1.198 | 0.60 |
| 114_G | 392_G | 1.195 | 0.59 |
| 134_E | 151_Y | 1.194 | 0.59 |
| 231_G | 265_G | 1.191 | 0.59 |
| 172_G | 231_G | 1.188 | 0.59 |
| 301_S | 381_I | 1.185 | 0.58 |
| 275_Y | 311_G | 1.180 | 0.58 |
| 141_K | 146_E | 1.177 | 0.58 |
| 163_W | 348_W | 1.169 | 0.57 |
| 216_N | 235_N | 1.169 | 0.57 |
| 275_Y | 286_G | 1.168 | 0.57 |
| 311_G | 323_G | 1.167 | 0.57 |
| 261_K | 279_W | 1.167 | 0.57 |
| 377_Q | 395_E | 1.167 | 0.57 |
| 161_G | 196_G | 1.165 | 0.57 |
| 139_Q | 146_E | 1.163 | 0.56 |
| 371_F | 376_R | 1.162 | 0.56 |
| 161_G | 208_G | 1.162 | 0.56 |
| 138_G | 185_G | 1.161 | 0.56 |
| 102_G | 149_G | 1.160 | 0.56 |
| 287_I | 301_S | 1.158 | 0.56 |
| 149_G | 196_G | 1.155 | 0.56 |
| 190_G | 233_W | 1.155 | 0.56 |
| 127_Y | 140_L | 1.154 | 0.55 |
| 330_K | 351_G | 1.151 | 0.55 |
| 189_N | 262_S | 1.150 | 0.55 |
| 163_W | 256_F | 1.150 | 0.55 |
| 262_S | 281_N | 1.138 | 0.54 |
| 231_G | 242_G | 1.134 | 0.53 |
| 83_Y | 279_W | 1.133 | 0.53 |
| 229_Y | 242_G | 1.123 | 0.52 |
| 193_S | 377_Q | 1.121 | 0.52 |
| 125_R | 185_G | 1.121 | 0.52 |
| 252_Y | 265_G | 1.120 | 0.52 |
| 101_K | 115_E | 1.113 | 0.51 |
| 302_F | 374_G | 1.110 | 0.51 |
| 102_G | 138_G | 1.110 | 0.51 |
| 137_E | 184_E | 1.109 | 0.51 |
| 208_G | 334_G | 1.103 | 0.50 |
| 277_G | 323_G | 1.100 | 0.50 |
| 186_E | 193_S | 1.100 | 0.50 |
| 192_K | 380_G | 1.096 | 0.50 |
| 239_H | 257_F | 1.092 | 0.49 |
| 334_G | 390_Y | 1.085 | 0.49 |
| 349_L | 395_E | 1.083 | 0.48 |
| 207_E | 381_I | 1.076 | 0.48 |
| 174_Y | 187_W | 1.075 | 0.48 |
| 344_Y | 413_V | 1.074 | 0.47 |
| 149_G | 265_G | 1.074 | 0.47 |
| 112_Y | 367_Y | 1.072 | 0.47 |
| 112_Y | 138_G | 1.071 | 0.47 |
| 300_G | 403_G | 1.067 | 0.47 |
| 168_K | 353_K | 1.067 | 0.47 |
| 355_G | 378_G | 1.067 | 0.47 |
| 413_V | 422_F | 1.065 | 0.47 |
| 277_G | 288_G | 1.062 | 0.46 |
| 150_K | 160_E | 1.059 | 0.46 |
| 115_E | 324_E | 1.056 | 0.46 |
| 179_S | 202_Y | 1.055 | 0.46 |
| 161_G | 185_G | 1.054 | 0.46 |
| 266_V | 276_D | 1.048 | 0.45 |
| 114_G | 138_G | 1.048 | 0.45 |
| 172_G | 185_G | 1.045 | 0.45 |
| 352_R | 373_A | 1.043 | 0.44 |
| 357_G | 369_G | 1.041 | 0.44 |
| 276_D | 289_T | 1.040 | 0.44 |
| 274_R | 412_I | 1.039 | 0.44 |
| 125_R | 172_G | 1.039 | 0.44 |
| 138_G | 161_G | 1.038 | 0.44 |
| 243_V | 251_R | 1.035 | 0.44 |
| 138_G | 196_G | 1.035 | 0.44 |
| 138_G | 265_G | 1.032 | 0.43 |
| 146_E | 164_F | 1.030 | 0.43 |
| 176_Y | 183_Y | 1.028 | 0.43 |
| 149_G | 161_G | 1.026 | 0.43 |
| 242_G | 288_G | 1.026 | 0.43 |
| 334_G | 415_G | 1.023 | 0.42 |
| 114_G | 185_G | 1.022 | 0.42 |
| 102_G | 125_R | 1.019 | 0.42 |
| 155_N | 181_E | 1.018 | 0.42 |
| 110_D | 256_F | 1.015 | 0.42 |
| 154_P | 408_A | 1.015 | 0.42 |
| 161_G | 183_Y | 1.015 | 0.42 |
| 161_G | 172_G | 1.013 | 0.42 |
| 121_F | 140_L | 1.013 | 0.42 |
| 268_T | 383_T | 1.011 | 0.41 |
| 381_I | 404_I | 1.011 | 0.41 |
| 125_R | 196_G | 1.010 | 0.41 |
| 95_G | 404_I | 1.006 | 0.41 |
| 321_Y | 390_Y | 1.004 | 0.41 |
| 106_Y | 246_C | 1.003 | 0.41 |
| 172_G | 380_G | 1.000 | 0.40 |
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 | |
| 1h3iA | 2 | 0.3474 | 100 | 0.786 | Contact Map |
| 2f69A | 1 | 0.1549 | 99.3 | 0.892 | Contact Map |
| 4ld1A | 1 | 0.3333 | 98.7 | 0.915 | Contact Map |
| 4by2A | 3 | 0.3404 | 97.8 | 0.933 | Contact Map |
| 4cnlA | 1 | 0.4249 | 89.2 | 0.96 | Contact Map |
| 2ww5A | 1 | 0.5 | 73.7 | 0.966 | Contact Map |
| 4tvcA | 1 | 0 | 59.9 | 0.969 | Contact Map |
| 3hiaA | 3 | 0.1948 | 6 | 0.982 | Contact Map |
| 1wlmA | 1 | 0.2277 | 5.8 | 0.982 | Contact Map |
| 1pulA | 1 | 0.1643 | 5.7 | 0.982 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)