| LAT1 sequence restraints |
| ID: | 1482144628 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 507 (445) | ||
| Sequences: | 12276 (6963) | ||
| Seq/Len: | 27.587 | ||
| Nf(neff/√len): | 330.1 |
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: 27.587).
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 |
| 183_T | 381_C | 4.513 | 1.00 |
| 93_G | 286_T | 3.801 | 1.00 |
| 362_I | 375_P | 3.735 | 1.00 |
| 52_L | 280_I | 3.449 | 1.00 |
| 56_V | 280_I | 3.239 | 1.00 |
| 354_S | 364_S | 3.228 | 1.00 |
| 272_R | 276_L | 3.194 | 1.00 |
| 367_H | 370_L | 3.170 | 1.00 |
| 417_W | 421_R | 2.884 | 1.00 |
| 267_M | 273_N | 2.829 | 1.00 |
| 117_Y | 356_E | 2.787 | 1.00 |
| 52_L | 273_N | 2.763 | 1.00 |
| 365_M | 375_P | 2.755 | 1.00 |
| 367_H | 374_V | 2.729 | 1.00 |
| 351_F | 355_R | 2.634 | 1.00 |
| 265_E | 355_R | 2.622 | 1.00 |
| 51_T | 268_I | 2.601 | 1.00 |
| 266_E | 348_R | 2.574 | 1.00 |
| 378_V | 382_V | 2.564 | 1.00 |
| 134_W | 468_G | 2.561 | 1.00 |
| 409_A | 440_I | 2.519 | 1.00 |
| 269_N | 272_R | 2.478 | 1.00 |
| 133_L | 353_G | 2.440 | 1.00 |
| 184_A | 188_Y | 2.413 | 1.00 |
| 55_G | 267_M | 2.402 | 1.00 |
| 269_N | 276_L | 2.377 | 1.00 |
| 362_I | 365_M | 2.375 | 1.00 |
| 187_C | 374_V | 2.365 | 1.00 |
| 215_G | 295_A | 2.348 | 1.00 |
| 276_L | 280_I | 2.318 | 1.00 |
| 301_S | 304_Q | 2.311 | 1.00 |
| 413_I | 440_I | 2.303 | 1.00 |
| 412_I | 439_F | 2.293 | 1.00 |
| 437_V | 441_L | 2.264 | 1.00 |
| 52_L | 56_V | 2.235 | 1.00 |
| 279_I | 283_P | 2.142 | 1.00 |
| 183_T | 377_L | 2.130 | 1.00 |
| 176_C | 388_A | 2.087 | 1.00 |
| 50_I | 54_N | 2.083 | 1.00 |
| 105_E | 419_R | 2.066 | 1.00 |
| 59_I | 281_S | 2.051 | 1.00 |
| 54_N | 198_D | 2.036 | 1.00 |
| 51_T | 54_N | 1.978 | 1.00 |
| 191_K | 195_R | 1.977 | 1.00 |
| 100_A | 282_L | 1.968 | 1.00 |
| 176_C | 385_L | 1.913 | 1.00 |
| 152_F | 332_G | 1.899 | 1.00 |
| 52_L | 276_L | 1.896 | 1.00 |
| 60_V | 284_I | 1.889 | 1.00 |
| 269_N | 273_N | 1.887 | 1.00 |
| 367_H | 372_T | 1.887 | 1.00 |
| 56_V | 284_I | 1.884 | 1.00 |
| 179_V | 381_C | 1.882 | 1.00 |
| 121_L | 129_A | 1.865 | 1.00 |
| 94_V | 98_V | 1.864 | 1.00 |
| 88_V | 246_A | 1.818 | 1.00 |
| 180_L | 381_C | 1.790 | 1.00 |
| 283_P | 287_L | 1.774 | 1.00 |
| 46_L | 366_I | 1.766 | 1.00 |
| 124_Y | 417_W | 1.762 | 1.00 |
| 357_G | 361_S | 1.742 | 1.00 |
| 95_F | 442_A | 1.700 | 1.00 |
| 462_F | 466_L | 1.696 | 1.00 |
| 109_T | 427_R | 1.692 | 1.00 |
| 202_A | 206_L | 1.689 | 1.00 |
| 63_I | 285_V | 1.689 | 1.00 |
| 263_V | 344_F | 1.685 | 1.00 |
| 108_T | 428_P | 1.668 | 1.00 |
| 187_C | 378_V | 1.662 | 1.00 |
| 370_L | 374_V | 1.659 | 1.00 |
| 188_Y | 370_L | 1.636 | 1.00 |
| 121_L | 126_S | 1.625 | 1.00 |
| 123_V | 414_G | 1.612 | 1.00 |
| 92_C | 250_G | 1.612 | 1.00 |
| 102_C | 412_I | 1.606 | 1.00 |
| 55_G | 277_A | 1.603 | 1.00 |
| 127_L | 469_L | 1.586 | 1.00 |
| 350_F | 376_S | 1.581 | 1.00 |
| 186_N | 340_N | 1.562 | 1.00 |
| 187_C | 372_T | 1.562 | 1.00 |
| 98_V | 438_F | 1.554 | 1.00 |
| 75_V | 85_A | 1.535 | 1.00 |
| 365_M | 374_V | 1.529 | 1.00 |
| 120_M | 132_K | 1.514 | 1.00 |
| 53_L | 57_A | 1.510 | 1.00 |
| 363_L | 379_F | 1.505 | 1.00 |
| 76_L | 85_A | 1.503 | 1.00 |
| 375_P | 379_F | 1.501 | 1.00 |
| 54_N | 194_T | 1.491 | 1.00 |
| 423_P | 427_R | 1.485 | 1.00 |
| 304_Q | 318_Y | 1.482 | 1.00 |
| 183_T | 187_C | 1.481 | 1.00 |
| 213_L | 217_V | 1.480 | 1.00 |
| 205_L | 288_V | 1.468 | 1.00 |
| 205_L | 209_A | 1.457 | 1.00 |
| 361_S | 365_M | 1.454 | 1.00 |
| 270_P | 275_P | 1.445 | 1.00 |
| 149_A | 339_V | 1.441 | 1.00 |
| 90_A | 290_V | 1.435 | 1.00 |
| 59_I | 260_L | 1.435 | 1.00 |
| 466_L | 470_P | 1.415 | 1.00 |
| 351_F | 366_I | 1.405 | 0.99 |
| 120_M | 410_L | 1.400 | 0.99 |
| 132_K | 410_L | 1.399 | 0.99 |
| 176_C | 180_L | 1.394 | 0.99 |
| 185_V | 196_V | 1.390 | 0.99 |
| 463_T | 467_S | 1.389 | 0.99 |
| 103_Y | 116_D | 1.380 | 0.99 |
| 152_F | 178_C | 1.369 | 0.99 |
| 113_S | 265_E | 1.367 | 0.99 |
| 112_K | 122_E | 1.366 | 0.99 |
| 470_P | 474_F | 1.363 | 0.99 |
| 413_I | 417_W | 1.350 | 0.99 |
| 100_A | 278_I | 1.347 | 0.99 |
| 125_G | 128_P | 1.346 | 0.99 |
| 50_I | 194_T | 1.342 | 0.99 |
| 273_N | 276_L | 1.326 | 0.99 |
| 109_T | 425_L | 1.315 | 0.99 |
| 441_L | 445_F | 1.315 | 0.99 |
| 50_I | 55_G | 1.313 | 0.99 |
| 264_T | 274_L | 1.311 | 0.99 |
| 57_A | 198_D | 1.298 | 0.99 |
| 382_V | 386_L | 1.298 | 0.99 |
| 183_T | 378_V | 1.295 | 0.99 |
| 182_L | 339_V | 1.290 | 0.99 |
| 347_S | 377_L | 1.286 | 0.99 |
| 215_G | 299_T | 1.282 | 0.99 |
| 153_A | 174_V | 1.281 | 0.99 |
| 212_I | 291_L | 1.270 | 0.99 |
| 216_F | 295_A | 1.270 | 0.99 |
| 70_V | 151_V | 1.270 | 0.99 |
| 346_S | 380_T | 1.266 | 0.99 |
| 124_Y | 413_I | 1.264 | 0.99 |
| 280_I | 284_I | 1.260 | 0.99 |
| 99_G | 412_I | 1.254 | 0.99 |
| 47_Q | 371_L | 1.237 | 0.98 |
| 122_E | 422_K | 1.236 | 0.98 |
| 244_V | 445_F | 1.235 | 0.98 |
| 101_L | 279_I | 1.232 | 0.98 |
| 120_M | 128_P | 1.231 | 0.98 |
| 58_I | 263_V | 1.225 | 0.98 |
| 460_I | 463_T | 1.223 | 0.98 |
| 46_L | 351_F | 1.218 | 0.98 |
| 175_A | 388_A | 1.213 | 0.98 |
| 46_L | 348_R | 1.209 | 0.98 |
| 350_F | 359_L | 1.206 | 0.98 |
| 52_L | 277_A | 1.201 | 0.98 |
| 93_G | 254_Y | 1.199 | 0.98 |
| 63_I | 281_S | 1.198 | 0.98 |
| 422_K | 425_L | 1.197 | 0.98 |
| 149_A | 179_V | 1.196 | 0.98 |
| 207_A | 330_F | 1.188 | 0.98 |
| 447_I | 459_G | 1.187 | 0.98 |
| 177_L | 181_L | 1.186 | 0.98 |
| 86_L | 294_L | 1.168 | 0.97 |
| 60_V | 285_V | 1.166 | 0.97 |
| 148_V | 338_S | 1.160 | 0.97 |
| 441_L | 444_L | 1.158 | 0.97 |
| 156_L | 332_G | 1.147 | 0.97 |
| 109_T | 428_P | 1.140 | 0.97 |
| 46_L | 49_N | 1.132 | 0.97 |
| 459_G | 463_T | 1.131 | 0.97 |
| 211_I | 215_G | 1.130 | 0.97 |
| 478_W | 481_K | 1.126 | 0.97 |
| 359_L | 363_L | 1.125 | 0.97 |
| 46_L | 266_E | 1.119 | 0.96 |
| 197_Q | 340_N | 1.117 | 0.96 |
| 418_L | 422_K | 1.117 | 0.96 |
| 182_L | 343_L | 1.114 | 0.96 |
| 200_F | 337_G | 1.114 | 0.96 |
| 196_V | 200_F | 1.100 | 0.96 |
| 86_L | 90_A | 1.095 | 0.96 |
| 84_L | 243_I | 1.082 | 0.96 |
| 184_A | 187_C | 1.081 | 0.95 |
| 53_L | 56_V | 1.081 | 0.95 |
| 91_A | 247_L | 1.081 | 0.95 |
| 105_E | 108_T | 1.078 | 0.95 |
| 117_Y | 352_V | 1.076 | 0.95 |
| 477_W | 481_K | 1.070 | 0.95 |
| 417_W | 420_H | 1.067 | 0.95 |
| 106_L | 415_M | 1.059 | 0.95 |
| 190_V | 344_F | 1.055 | 0.95 |
| 194_T | 198_D | 1.054 | 0.95 |
| 409_A | 413_I | 1.052 | 0.95 |
| 271_Y | 276_L | 1.045 | 0.94 |
| 116_D | 258_N | 1.042 | 0.94 |
| 48_R | 266_E | 1.042 | 0.94 |
| 180_L | 385_L | 1.029 | 0.94 |
| 49_N | 190_V | 1.022 | 0.93 |
| 204_K | 334_S | 1.020 | 0.93 |
| 239_D | 242_N | 1.020 | 0.93 |
| 179_V | 384_T | 1.018 | 0.93 |
| 287_L | 291_L | 1.018 | 0.93 |
| 291_L | 295_A | 1.016 | 0.93 |
| 112_K | 118_A | 1.013 | 0.93 |
| 187_C | 370_L | 1.006 | 0.93 |
| 68_I | 208_L | 1.006 | 0.93 |
| 124_Y | 128_P | 1.005 | 0.93 |
| 210_L | 214_L | 1.000 | 0.92 |
| 322_V | 326_I | 1.000 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3l1lA | 1 | 0.8185 | 100 | 0.471 | Contact Map |
| 3giaA | 1 | 0.8402 | 100 | 0.51 | Contact Map |
| 4djkA | 2 | 0.8047 | 100 | 0.523 | Contact Map |
| 2jlnA | 1 | 0.8442 | 98.7 | 0.894 | Contact Map |
| 3dh4A | 4 | 0.8422 | 98.2 | 0.91 | Contact Map |
| 2xq2A | 1 | 0.856 | 97.6 | 0.921 | Contact Map |
| 4wgvA | 2 | 0.7081 | 95.8 | 0.938 | Contact Map |
| 4xp4A | 1 | 0 | 92 | 0.947 | Contact Map |
| 2a65A | 1 | 0.8402 | 81.9 | 0.955 | Contact Map |
| 4us3A | 1 | 0.7613 | 73.3 | 0.959 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)