| TRPA1_s -force run |
| ID: | 1438081286 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 992 (548) | ||
| Sequences: | 16065 (12338.7) | ||
| Seq/Len: | 29.316 | ||
| Nf(neff/√len): | 527.1 |
HHblits Results: (2013_03)
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: 29.316).
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 |
| 282_E | 311_D | 2.798 | 1.00 |
| 315_R | 344_D | 2.664 | 1.00 |
| 297_A | 329_I | 2.543 | 1.00 |
| 212_A | 241_E | 2.494 | 1.00 |
| 386_C | 415_S | 2.482 | 1.00 |
| 227_I | 259_I | 2.481 | 1.00 |
| 455_M | 483_D | 2.246 | 1.00 |
| 521_N | 549_N | 2.210 | 1.00 |
| 138_N | 167_N | 2.203 | 1.00 |
| 434_C | 469_V | 2.200 | 1.00 |
| 245_C | 278_D | 2.195 | 1.00 |
| 502_M | 535_A | 2.186 | 1.00 |
| 487_W | 517_D | 2.171 | 1.00 |
| 51_M | 85_S | 2.171 | 1.00 |
| 260_V | 296_L | 2.125 | 1.00 |
| 119_M | 152_A | 2.069 | 1.00 |
| 171_C | 208_N | 2.010 | 1.00 |
| 286_H | 317_P | 1.986 | 1.00 |
| 71_N | 100_N | 1.960 | 1.00 |
| 419_K | 451_D | 1.958 | 1.00 |
| 292_D | 326_S | 1.938 | 1.00 |
| 86_V | 118_V | 1.907 | 1.00 |
| 223_D | 226_M | 1.896 | 1.00 |
| 104_M | 134_G | 1.865 | 1.00 |
| 299_Y | 303_V | 1.856 | 1.00 |
| 186_M | 226_M | 1.827 | 1.00 |
| 390_H | 421_P | 1.814 | 1.00 |
| 216_H | 247_A | 1.797 | 1.00 |
| 451_D | 455_M | 1.776 | 1.00 |
| 401_V | 433_T | 1.770 | 1.00 |
| 47_Q | 50_L | 1.768 | 1.00 |
| 81_N | 115_N | 1.724 | 1.00 |
| 459_H | 489_A | 1.715 | 1.00 |
| 423_H | 457_P | 1.706 | 1.00 |
| 318_L | 330_V | 1.699 | 1.00 |
| 255_G | 293_H | 1.698 | 1.00 |
| 75_H | 106_P | 1.694 | 1.00 |
| 415_S | 419_K | 1.681 | 1.00 |
| 319_I | 350_F | 1.679 | 1.00 |
| 311_D | 315_R | 1.677 | 1.00 |
| 222_G | 256_A | 1.674 | 1.00 |
| 315_R | 323_A | 1.663 | 1.00 |
| 219_V | 222_G | 1.659 | 1.00 |
| 114_M | 149_N | 1.656 | 1.00 |
| 470_V | 501_T | 1.652 | 1.00 |
| 249_H | 284_M | 1.644 | 1.00 |
| 326_S | 329_I | 1.635 | 1.00 |
| 90_L | 121_V | 1.626 | 1.00 |
| 332_L | 336_K | 1.602 | 1.00 |
| 403_N | 407_F | 1.599 | 1.00 |
| 78_V | 81_N | 1.593 | 1.00 |
| 229_M | 233_N | 1.577 | 1.00 |
| 252_A | 255_G | 1.576 | 1.00 |
| 215_L | 227_I | 1.575 | 1.00 |
| 483_D | 487_W | 1.574 | 1.00 |
| 123_L | 155_I | 1.569 | 1.00 |
| 322_T | 325_A | 1.562 | 1.00 |
| 141_V | 153_L | 1.560 | 1.00 |
| 153_L | 185_C | 1.560 | 1.00 |
| 525_H | 555_F | 1.553 | 1.00 |
| 149_N | 152_A | 1.542 | 1.00 |
| 491_H | 523_A | 1.540 | 1.00 |
| 257_T | 299_Y | 1.533 | 1.00 |
| 83_I | 121_V | 1.532 | 1.00 |
| 108_H | 140_A | 1.519 | 1.00 |
| 248_I | 260_V | 1.519 | 1.00 |
| 344_D | 348_R | 1.516 | 1.00 |
| 462_A | 465_G | 1.514 | 1.00 |
| 331_N | 335_S | 1.508 | 1.00 |
| 36_T | 67_D | 1.506 | 1.00 |
| 458_L | 470_V | 1.505 | 1.00 |
| 82_Q | 85_S | 1.504 | 1.00 |
| 142_I | 173_P | 1.504 | 1.00 |
| 298_D | 332_L | 1.503 | 1.00 |
| 397_G | 400_S | 1.497 | 1.00 |
| 289_S | 292_D | 1.482 | 1.00 |
| 278_D | 282_E | 1.478 | 1.00 |
| 157_L | 163_P | 1.478 | 1.00 |
| 231_L | 262_L | 1.477 | 1.00 |
| 517_D | 521_N | 1.476 | 1.00 |
| 182_S | 185_C | 1.464 | 1.00 |
| 241_E | 245_C | 1.457 | 1.00 |
| 46_G | 82_Q | 1.453 | 1.00 |
| 422_L | 434_C | 1.452 | 1.00 |
| 175_H | 214_P | 1.451 | 1.00 |
| 461_A | 470_V | 1.450 | 1.00 |
| 321_A | 330_V | 1.449 | 1.00 |
| 145_C | 148_N | 1.448 | 1.00 |
| 155_I | 159_K | 1.448 | 1.00 |
| 100_N | 109_I | 1.448 | 1.00 |
| 557_H | 560_L | 1.443 | 1.00 |
| 110_A | 119_M | 1.442 | 1.00 |
| 111_V | 114_M | 1.438 | 1.00 |
| 490_L | 502_M | 1.437 | 1.00 |
| 256_A | 259_I | 1.432 | 1.00 |
| 301_I | 332_L | 1.431 | 1.00 |
| 224_L | 262_L | 1.430 | 1.00 |
| 472_L | 476_K | 1.425 | 1.00 |
| 257_T | 261_K | 1.419 | 1.00 |
| 74_L | 86_V | 1.416 | 1.00 |
| 282_E | 290_L | 1.415 | 1.00 |
| 148_N | 182_S | 1.413 | 1.00 |
| 88_F | 92_R | 1.406 | 0.99 |
| 348_R | 382_D | 1.402 | 0.99 |
| 104_M | 112_Q | 1.397 | 0.99 |
| 429_G | 466_H | 1.396 | 0.99 |
| 115_N | 118_V | 1.386 | 0.99 |
| 178_A | 181_G | 1.385 | 0.99 |
| 224_L | 258_E | 1.384 | 0.99 |
| 294_H | 332_L | 1.382 | 0.99 |
| 264_I | 299_Y | 1.380 | 0.99 |
| 208_N | 212_A | 1.378 | 0.99 |
| 430_R | 433_T | 1.378 | 0.99 |
| 289_S | 329_I | 1.377 | 0.99 |
| 426_A | 429_G | 1.375 | 0.99 |
| 224_L | 228_K | 1.365 | 0.99 |
| 327_W | 331_N | 1.364 | 0.99 |
| 334_L | 340_V | 1.362 | 0.99 |
| 398_P | 402_N | 1.359 | 0.99 |
| 310_I | 342_I | 1.354 | 0.99 |
| 40_H | 73_P | 1.354 | 0.99 |
| 285_L | 297_A | 1.352 | 0.99 |
| 301_I | 336_K | 1.347 | 0.99 |
| 294_H | 298_D | 1.347 | 0.99 |
| 144_A | 153_L | 1.343 | 0.99 |
| 121_V | 125_H | 1.338 | 0.99 |
| 87_K | 91_S | 1.338 | 0.99 |
| 293_H | 296_L | 1.334 | 0.99 |
| 322_T | 330_V | 1.321 | 0.99 |
| 498_Y | 501_T | 1.321 | 0.99 |
| 528_A | 531_G | 1.319 | 0.99 |
| 181_G | 223_D | 1.314 | 0.99 |
| 43_A | 46_G | 1.314 | 0.99 |
| 134_G | 138_N | 1.311 | 0.99 |
| 289_S | 297_A | 1.309 | 0.99 |
| 100_N | 104_M | 1.305 | 0.99 |
| 219_V | 259_I | 1.303 | 0.99 |
| 382_D | 386_C | 1.303 | 0.99 |
| 455_M | 463_K | 1.301 | 0.99 |
| 67_D | 71_N | 1.291 | 0.99 |
| 396_G | 430_R | 1.289 | 0.99 |
| 212_A | 220_Q | 1.289 | 0.99 |
| 301_I | 307_I | 1.286 | 0.99 |
| 294_H | 329_I | 1.286 | 0.99 |
| 459_H | 491_H | 1.285 | 0.99 |
| 471_Q | 475_K | 1.284 | 0.99 |
| 262_L | 266_S | 1.284 | 0.99 |
| 193_G | 202_L | 1.282 | 0.99 |
| 219_V | 227_I | 1.279 | 0.99 |
| 138_N | 146_T | 1.279 | 0.99 |
| 465_G | 498_Y | 1.278 | 0.99 |
| 302_S | 336_K | 1.277 | 0.99 |
| 251_A | 260_V | 1.276 | 0.99 |
| 53_K | 57_D | 1.276 | 0.99 |
| 311_D | 320_L | 1.274 | 0.99 |
| 389_L | 401_V | 1.273 | 0.99 |
| 521_N | 529_R | 1.266 | 0.99 |
| 218_A | 227_I | 1.262 | 0.99 |
| 107_L | 119_M | 1.262 | 0.99 |
| 77_A | 86_V | 1.258 | 0.99 |
| 419_K | 427_S | 1.258 | 0.99 |
| 257_T | 295_E | 1.254 | 0.99 |
| 438_L | 472_L | 1.251 | 0.99 |
| 241_E | 250_F | 1.249 | 0.99 |
| 467_D | 471_Q | 1.249 | 0.99 |
| 228_K | 262_L | 1.249 | 0.99 |
| 134_G | 143_I | 1.247 | 0.99 |
| 497_G | 532_H | 1.246 | 0.98 |
| 42_A | 51_M | 1.246 | 0.98 |
| 294_H | 328_N | 1.242 | 0.98 |
| 111_V | 152_A | 1.240 | 0.98 |
| 487_W | 495_M | 1.236 | 0.98 |
| 261_K | 299_Y | 1.231 | 0.98 |
| 189_I | 193_G | 1.230 | 0.98 |
| 494_S | 497_G | 1.230 | 0.98 |
| 167_N | 171_C | 1.230 | 0.98 |
| 506_L | 538_L | 1.225 | 0.98 |
| 402_N | 436_R | 1.223 | 0.98 |
| 188_I | 192_F | 1.214 | 0.98 |
| 78_V | 118_V | 1.213 | 0.98 |
| 171_C | 179_F | 1.207 | 0.98 |
| 183_K | 187_E | 1.206 | 0.98 |
| 39_L | 51_M | 1.205 | 0.98 |
| 116_N | 120_K | 1.203 | 0.98 |
| 154_Q | 158_K | 1.202 | 0.98 |
| 83_I | 87_K | 1.193 | 0.98 |
| 517_D | 526_F | 1.193 | 0.98 |
| 216_H | 250_F | 1.193 | 0.98 |
| 524_L | 536_V | 1.193 | 0.98 |
| 435_Q | 439_Q | 1.192 | 0.98 |
| 120_K | 155_I | 1.192 | 0.98 |
| 298_D | 302_S | 1.192 | 0.98 |
| 252_A | 296_L | 1.191 | 0.98 |
| 228_K | 232_D | 1.189 | 0.98 |
| 431_I | 435_Q | 1.185 | 0.98 |
| 386_C | 394_R | 1.184 | 0.98 |
| 278_D | 287_R | 1.183 | 0.98 |
| 83_I | 117_E | 1.180 | 0.98 |
| 224_L | 259_I | 1.173 | 0.98 |
| 288_A | 297_A | 1.172 | 0.98 |
| 245_C | 253_T | 1.172 | 0.98 |
| 527_A | 536_V | 1.170 | 0.97 |
| 167_N | 176_Q | 1.164 | 0.97 |
| 116_N | 151_E | 1.158 | 0.97 |
| 435_Q | 472_L | 1.157 | 0.97 |
| 536_V | 567_V | 1.157 | 0.97 |
| 425_A | 434_C | 1.156 | 0.97 |
| 55_T | 88_F | 1.155 | 0.97 |
| 116_N | 155_I | 1.154 | 0.97 |
| 150_S | 154_Q | 1.154 | 0.97 |
| 71_N | 79_E | 1.154 | 0.97 |
| 431_I | 472_L | 1.154 | 0.97 |
| 213_T | 216_H | 1.150 | 0.97 |
| 43_A | 85_S | 1.146 | 0.97 |
| 393_C | 396_G | 1.136 | 0.97 |
| 48_I | 52_E | 1.135 | 0.97 |
| 494_S | 535_A | 1.129 | 0.97 |
| 439_Q | 476_K | 1.126 | 0.97 |
| 459_H | 462_A | 1.122 | 0.97 |
| 532_H | 535_A | 1.121 | 0.97 |
| 90_L | 96_P | 1.120 | 0.96 |
| 231_L | 237_I | 1.118 | 0.96 |
| 246_T | 249_H | 1.118 | 0.96 |
| 451_D | 460_L | 1.116 | 0.96 |
| 286_H | 319_I | 1.115 | 0.96 |
| 549_N | 553_A | 1.114 | 0.96 |
| 474_L | 504_V | 1.113 | 0.96 |
| 207_M | 239_P | 1.113 | 0.96 |
| 525_H | 528_A | 1.112 | 0.96 |
| 423_H | 459_H | 1.112 | 0.96 |
| 538_L | 542_H | 1.112 | 0.96 |
| 257_T | 296_L | 1.111 | 0.96 |
| 415_S | 424_F | 1.111 | 0.96 |
| 252_A | 260_V | 1.109 | 0.96 |
| 87_K | 121_V | 1.103 | 0.96 |
| 405_L | 436_R | 1.103 | 0.96 |
| 50_L | 53_K | 1.101 | 0.96 |
| 208_N | 217_L | 1.100 | 0.96 |
| 537_A | 541_S | 1.100 | 0.96 |
| 219_V | 256_A | 1.097 | 0.96 |
| 67_D | 76_C | 1.096 | 0.96 |
| 489_A | 505_I | 1.093 | 0.96 |
| 390_H | 423_H | 1.092 | 0.96 |
| 285_L | 301_I | 1.090 | 0.96 |
| 344_D | 353_L | 1.087 | 0.96 |
| 467_D | 501_T | 1.085 | 0.96 |
| 174_I | 186_M | 1.084 | 0.96 |
| 549_N | 558_L | 1.081 | 0.95 |
| 483_D | 492_H | 1.080 | 0.95 |
| 374_I | 377_L | 1.080 | 0.95 |
| 528_A | 536_V | 1.077 | 0.95 |
| 364_L | 368_F | 1.076 | 0.95 |
| 111_V | 119_M | 1.073 | 0.95 |
| 503_K | 507_D | 1.073 | 0.95 |
| 277_T | 309_K | 1.072 | 0.95 |
| 352_H | 355_V | 1.071 | 0.95 |
| 504_V | 508_T | 1.068 | 0.95 |
| 145_C | 153_L | 1.066 | 0.95 |
| 462_A | 501_T | 1.066 | 0.95 |
| 249_H | 286_H | 1.065 | 0.95 |
| 462_A | 470_V | 1.059 | 0.95 |
| 531_G | 564_R | 1.058 | 0.95 |
| 316_S | 319_I | 1.055 | 0.95 |
| 393_C | 433_T | 1.054 | 0.95 |
| 352_H | 388_P | 1.051 | 0.94 |
| 466_H | 469_V | 1.049 | 0.94 |
| 560_L | 563_K | 1.048 | 0.94 |
| 410_S | 413_S | 1.046 | 0.94 |
| 467_D | 504_V | 1.045 | 0.94 |
| 241_E | 244_R | 1.044 | 0.94 |
| 431_I | 469_V | 1.042 | 0.94 |
| 308_N | 338_A | 1.041 | 0.94 |
| 404_L | 409_V | 1.041 | 0.94 |
| 286_H | 320_L | 1.041 | 0.94 |
| 398_P | 436_R | 1.040 | 0.94 |
| 283_T | 286_H | 1.040 | 0.94 |
| 215_L | 231_L | 1.039 | 0.94 |
| 392_A | 401_V | 1.037 | 0.94 |
| 58_S | 61_E | 1.033 | 0.94 |
| 308_N | 342_I | 1.029 | 0.94 |
| 402_N | 406_G | 1.029 | 0.94 |
| 499_T | 538_L | 1.027 | 0.94 |
| 436_R | 440_D | 1.022 | 0.93 |
| 365_R | 368_F | 1.022 | 0.93 |
| 36_T | 44_A | 1.022 | 0.93 |
| 123_L | 130_V | 1.020 | 0.93 |
| 157_L | 188_I | 1.020 | 0.93 |
| 471_Q | 504_V | 1.018 | 0.93 |
| 350_F | 354_T | 1.017 | 0.93 |
| 150_S | 184_E | 1.015 | 0.93 |
| 75_H | 108_H | 1.014 | 0.93 |
| 306_D | 309_K | 1.012 | 0.93 |
| 390_H | 459_H | 1.011 | 0.93 |
| 78_V | 106_P | 1.011 | 0.93 |
| 423_H | 460_L | 1.010 | 0.93 |
| 426_A | 469_V | 1.010 | 0.93 |
| 236_Q | 239_P | 1.009 | 0.93 |
| 499_T | 503_K | 1.005 | 0.93 |
| 553_A | 561_H | 1.003 | 0.93 |
| 414_K | 449_E | 1.003 | 0.93 |
| 505_I | 510_L | 1.003 | 0.93 |
| 232_D | 266_S | 1.003 | 0.93 |
| 105_A | 108_H | 1.002 | 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 | |
| 4rlvA | 1 | 0.5877 | 100 | 0.526 | Contact Map |
| 4cj9A | 2 | 0.5867 | 100 | 0.549 | Contact Map |
| 3j5pB | 4 | 0.5484 | 100 | 0.616 | Contact Map |
| 1n11A | 1 | 0.4073 | 100 | 0.658 | Contact Map |
| 3ljnA | 1 | 0.2732 | 100 | 0.747 | Contact Map |
| 3utmA | 2 | 0.3196 | 100 | 0.751 | Contact Map |
| 4rlyA | 1 | 0.3044 | 100 | 0.753 | Contact Map |
| 4oavB | 2 | 0.621 | 100 | 0.756 | Contact Map |
| 4ot9A | 1 | 0.2843 | 100 | 0.77 | Contact Map |
| 1wdyA | 1 | 0.2802 | 100 | 0.778 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)