| 1G6S |
| ID: | 1470063003 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 427 (424) | ||
| Sequences: | 6473 (3596.9) | ||
| Seq/Len: | 15.267 | ||
| Nf(neff/√len): | 174.7 |
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: 15.267).
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 |
| 259_T | 295_S | 4.290 | 1.00 |
| 15_T | 263_T | 3.959 | 1.00 |
| 358_E | 369_T | 3.803 | 1.00 |
| 42_T | 238_L | 3.334 | 1.00 |
| 261_K | 295_S | 3.326 | 1.00 |
| 413_F | 419_Q | 3.234 | 1.00 |
| 351_E | 354_K | 3.135 | 1.00 |
| 380_A | 404_L | 3.087 | 1.00 |
| 116_T | 122_K | 3.013 | 1.00 |
| 161_N | 190_R | 2.989 | 1.00 |
| 415_D | 418_E | 2.900 | 1.00 |
| 17_N | 263_T | 2.793 | 1.00 |
| 328_T | 369_T | 2.763 | 1.00 |
| 55_N | 58_T | 2.696 | 1.00 |
| 251_A | 321_A | 2.535 | 1.00 |
| 208_M | 213_V | 2.522 | 1.00 |
| 260_V | 423_I | 2.456 | 1.00 |
| 351_E | 391_F | 2.383 | 1.00 |
| 259_T | 297_T | 2.376 | 1.00 |
| 254_A | 285_A | 2.364 | 1.00 |
| 305_D | 332_R | 2.307 | 1.00 |
| 169_S | 172_F | 2.253 | 1.00 |
| 40_V | 74_E | 2.251 | 1.00 |
| 214_E | 226_K | 2.238 | 1.00 |
| 25_S | 44_L | 2.213 | 1.00 |
| 395_A | 401_V | 2.212 | 1.00 |
| 38_K | 76_I | 2.203 | 1.00 |
| 352_L | 357_A | 2.171 | 1.00 |
| 56_A | 90_L | 2.149 | 1.00 |
| 378_E | 404_L | 2.142 | 1.00 |
| 320_T | 390_C | 2.136 | 1.00 |
| 46_D | 51_R | 2.112 | 1.00 |
| 104_A | 175_A | 2.103 | 1.00 |
| 65_T | 74_E | 2.074 | 1.00 |
| 351_E | 382_Y | 2.074 | 1.00 |
| 255_I | 393_L | 2.038 | 1.00 |
| 46_D | 66_L | 2.034 | 1.00 |
| 355_V | 401_V | 2.006 | 1.00 |
| 42_T | 236_T | 2.000 | 1.00 |
| 13_D | 259_T | 1.995 | 1.00 |
| 159_G | 183_A | 1.988 | 1.00 |
| 132_A | 176_L | 1.977 | 1.00 |
| 29_L | 57_L | 1.965 | 1.00 |
| 177_L | 205_L | 1.956 | 1.00 |
| 127_G | 131_D | 1.954 | 1.00 |
| 338_R | 343_D | 1.947 | 1.00 |
| 161_N | 188_V | 1.934 | 1.00 |
| 324_F | 397_S | 1.916 | 1.00 |
| 360_E | 367_R | 1.906 | 1.00 |
| 286_T | 297_T | 1.896 | 1.00 |
| 41_L | 75_I | 1.893 | 1.00 |
| 322_A | 329_T | 1.856 | 1.00 |
| 305_D | 330_T | 1.856 | 1.00 |
| 163_D | 190_R | 1.855 | 1.00 |
| 303_A | 329_T | 1.823 | 1.00 |
| 139_K | 154_Q | 1.800 | 1.00 |
| 32_A | 39_T | 1.799 | 1.00 |
| 378_E | 402_T | 1.792 | 1.00 |
| 186_D | 226_K | 1.788 | 1.00 |
| 330_T | 367_R | 1.761 | 1.00 |
| 323_L | 357_A | 1.755 | 1.00 |
| 63_S | 76_I | 1.744 | 1.00 |
| 120_R | 123_E | 1.733 | 1.00 |
| 250_L | 280_L | 1.693 | 1.00 |
| 30_L | 53_M | 1.692 | 1.00 |
| 349_A | 359_V | 1.684 | 1.00 |
| 15_T | 261_K | 1.677 | 1.00 |
| 288_C | 295_S | 1.675 | 1.00 |
| 355_V | 394_V | 1.672 | 1.00 |
| 40_V | 72_R | 1.661 | 1.00 |
| 379_I | 391_F | 1.651 | 1.00 |
| 28_A | 207_L | 1.649 | 1.00 |
| 347_A | 382_Y | 1.620 | 1.00 |
| 360_E | 369_T | 1.606 | 1.00 |
| 278_D | 281_E | 1.603 | 1.00 |
| 110_S | 152_R | 1.602 | 1.00 |
| 42_T | 72_R | 1.601 | 1.00 |
| 130_V | 142_Y | 1.588 | 1.00 |
| 54_L | 64_Y | 1.584 | 1.00 |
| 328_T | 367_R | 1.559 | 1.00 |
| 290_G | 295_S | 1.552 | 1.00 |
| 300_E | 326_K | 1.547 | 1.00 |
| 95_A | 98_A | 1.543 | 1.00 |
| 319_A | 348_M | 1.542 | 1.00 |
| 343_D | 346_F | 1.530 | 1.00 |
| 252_A | 396_L | 1.522 | 1.00 |
| 131_D | 135_L | 1.512 | 1.00 |
| 89_E | 114_V | 1.503 | 1.00 |
| 99_M | 149_P | 1.502 | 1.00 |
| 156_G | 184_P | 1.494 | 1.00 |
| 190_R | 222_Q | 1.488 | 1.00 |
| 58_T | 64_Y | 1.486 | 1.00 |
| 349_A | 366_I | 1.483 | 1.00 |
| 357_A | 374_L | 1.478 | 1.00 |
| 261_K | 290_G | 1.474 | 1.00 |
| 249_F | 413_F | 1.463 | 1.00 |
| 419_Q | 422_R | 1.449 | 1.00 |
| 44_L | 50_V | 1.448 | 1.00 |
| 247_S | 314_A | 1.422 | 1.00 |
| 202_D | 206_N | 1.420 | 1.00 |
| 303_A | 328_T | 1.419 | 1.00 |
| 28_A | 239_V | 1.418 | 1.00 |
| 29_L | 54_L | 1.417 | 1.00 |
| 26_N | 53_M | 1.412 | 1.00 |
| 320_T | 394_V | 1.409 | 1.00 |
| 240_E | 269_S | 1.405 | 0.99 |
| 346_F | 350_T | 1.404 | 0.99 |
| 307_D | 333_N | 1.399 | 0.99 |
| 355_V | 377_A | 1.393 | 0.99 |
| 246_A | 265_I | 1.387 | 0.99 |
| 141_T | 154_Q | 1.374 | 0.99 |
| 92_L | 121_M | 1.373 | 0.99 |
| 319_A | 331_L | 1.364 | 0.99 |
| 357_A | 371_P | 1.359 | 0.99 |
| 112_D | 150_P | 1.358 | 0.99 |
| 65_T | 76_I | 1.357 | 0.99 |
| 252_A | 393_L | 1.356 | 0.99 |
| 388_A | 408_C | 1.356 | 0.99 |
| 133_L | 138_A | 1.348 | 0.99 |
| 209_K | 218_Q | 1.341 | 0.99 |
| 66_L | 73_C | 1.339 | 0.99 |
| 327_G | 370_P | 1.333 | 0.99 |
| 218_Q | 223_F | 1.325 | 0.99 |
| 52_H | 93_G | 1.320 | 0.99 |
| 141_T | 152_R | 1.319 | 0.99 |
| 35_A | 39_T | 1.316 | 0.99 |
| 17_N | 264_G | 1.304 | 0.99 |
| 392_S | 416_Y | 1.297 | 0.99 |
| 58_T | 63_S | 1.295 | 0.99 |
| 134_R | 139_K | 1.295 | 0.99 |
| 279_V | 318_I | 1.287 | 0.99 |
| 280_L | 285_A | 1.274 | 0.99 |
| 177_L | 225_V | 1.268 | 0.99 |
| 247_S | 317_T | 1.264 | 0.99 |
| 7_Q | 400_P | 1.257 | 0.99 |
| 250_L | 277_A | 1.257 | 0.99 |
| 283_M | 325_A | 1.256 | 0.99 |
| 302_N | 326_K | 1.252 | 0.99 |
| 18_L | 262_V | 1.250 | 0.99 |
| 280_L | 321_A | 1.248 | 0.99 |
| 48_D | 410_A | 1.239 | 0.98 |
| 28_A | 41_L | 1.238 | 0.98 |
| 38_K | 74_E | 1.236 | 0.98 |
| 362_G | 365_Y | 1.229 | 0.98 |
| 55_N | 59_A | 1.228 | 0.98 |
| 251_A | 276_F | 1.226 | 0.98 |
| 67_S | 74_E | 1.223 | 0.98 |
| 243_A | 276_F | 1.216 | 0.98 |
| 163_D | 192_K | 1.209 | 0.98 |
| 379_I | 401_V | 1.207 | 0.98 |
| 40_V | 236_T | 1.207 | 0.98 |
| 388_A | 409_T | 1.205 | 0.98 |
| 25_S | 45_L | 1.196 | 0.98 |
| 250_L | 262_V | 1.191 | 0.98 |
| 100_R | 174_T | 1.186 | 0.98 |
| 131_D | 134_R | 1.186 | 0.98 |
| 56_A | 92_L | 1.184 | 0.98 |
| 25_S | 50_V | 1.182 | 0.98 |
| 205_L | 215_I | 1.182 | 0.98 |
| 216_E | 226_K | 1.173 | 0.98 |
| 353_R | 358_E | 1.159 | 0.97 |
| 130_V | 134_R | 1.154 | 0.97 |
| 283_M | 304_I | 1.154 | 0.97 |
| 62_V | 75_I | 1.153 | 0.97 |
| 16_I | 423_I | 1.147 | 0.97 |
| 14_G | 423_I | 1.143 | 0.97 |
| 331_L | 366_I | 1.138 | 0.97 |
| 398_D | 401_V | 1.136 | 0.97 |
| 140_I | 151_L | 1.132 | 0.97 |
| 250_L | 253_A | 1.129 | 0.97 |
| 52_H | 55_N | 1.125 | 0.97 |
| 41_L | 239_V | 1.125 | 0.97 |
| 195_L | 201_I | 1.122 | 0.97 |
| 57_L | 62_V | 1.121 | 0.97 |
| 348_M | 387_M | 1.116 | 0.96 |
| 380_A | 405_D | 1.116 | 0.96 |
| 180_A | 187_T | 1.114 | 0.96 |
| 29_L | 75_I | 1.102 | 0.96 |
| 405_D | 408_C | 1.102 | 0.96 |
| 189_I | 192_K | 1.100 | 0.96 |
| 334_I | 365_Y | 1.099 | 0.96 |
| 415_D | 419_Q | 1.099 | 0.96 |
| 345_L | 366_I | 1.098 | 0.96 |
| 205_L | 218_Q | 1.097 | 0.96 |
| 12_V | 252_A | 1.091 | 0.96 |
| 129_L | 175_A | 1.089 | 0.96 |
| 279_V | 306_M | 1.089 | 0.96 |
| 362_G | 367_R | 1.085 | 0.96 |
| 359_V | 366_I | 1.084 | 0.96 |
| 418_E | 421_A | 1.080 | 0.95 |
| 58_T | 66_L | 1.078 | 0.95 |
| 346_F | 361_E | 1.076 | 0.95 |
| 188_V | 224_V | 1.060 | 0.95 |
| 354_K | 377_A | 1.060 | 0.95 |
| 174_T | 204_T | 1.060 | 0.95 |
| 33_A | 57_L | 1.049 | 0.94 |
| 349_A | 361_E | 1.049 | 0.94 |
| 126_I | 130_V | 1.047 | 0.94 |
| 275_R | 278_D | 1.047 | 0.94 |
| 322_A | 331_L | 1.042 | 0.94 |
| 207_L | 211_F | 1.037 | 0.94 |
| 57_L | 64_Y | 1.034 | 0.94 |
| 51_R | 66_L | 1.030 | 0.94 |
| 157_F | 183_A | 1.026 | 0.94 |
| 54_L | 58_T | 1.025 | 0.93 |
| 279_V | 311_I | 1.023 | 0.93 |
| 89_E | 116_T | 1.022 | 0.93 |
| 34_L | 105_A | 1.017 | 0.93 |
| 251_A | 280_L | 1.017 | 0.93 |
| 40_V | 235_G | 1.017 | 0.93 |
| 213_V | 230_S | 1.013 | 0.93 |
| 42_T | 237_Y | 1.004 | 0.93 |
| 5_T | 400_P | 1.001 | 0.92 |
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 | |
| 3rmtA | 4 | 0.9672 | 100 | 0.068 | Contact Map |
| 3nvsA | 1 | 0.993 | 100 | 0.086 | Contact Map |
| 2pqcA | 1 | 0.9696 | 100 | 0.093 | Contact Map |
| 3slhA | 4 | 0.9672 | 100 | 0.116 | Contact Map |
| 1rf6A | 4 | 0.9625 | 100 | 0.124 | Contact Map |
| 2o0bA | 1 | 0.9625 | 100 | 0.131 | Contact Map |
| 3zh4A | 1 | 0.9297 | 100 | 0.221 | Contact Map |
| 4fqdA | 2 | 0.9368 | 100 | 0.227 | Contact Map |
| 3r38A | 1 | 0.9391 | 100 | 0.23 | Contact Map |
| 1ejdA | 2 | 0.9438 | 100 | 0.249 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)