| hNav15-DIII-IV |
| ID: | 1500065841 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 822 (672) | ||
| Sequences: | 2759 (1638) | ||
| Seq/Len: | 4.106 | ||
| Nf(neff/√len): | 63.2 |
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: 4.106).
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 |
| 477_Y | 560_T | 5.933 | 1.00 |
| 331_V | 383_V | 2.975 | 1.00 |
| 59_E | 63_K | 2.896 | 1.00 |
| 381_C | 392_Y | 2.740 | 1.00 |
| 154_F | 258_I | 2.709 | 1.00 |
| 331_V | 336_F | 2.686 | 1.00 |
| 432_R | 435_R | 2.529 | 1.00 |
| 355_T | 362_K | 2.436 | 1.00 |
| 380_E | 384_K | 2.426 | 1.00 |
| 393_F | 402_F | 2.386 | 1.00 |
| 381_C | 402_F | 2.333 | 1.00 |
| 166_F | 234_A | 2.328 | 1.00 |
| 72_Y | 81_D | 2.318 | 1.00 |
| 234_A | 256_F | 2.308 | 1.00 |
| 57_V | 89_L | 2.279 | 1.00 |
| 482_M | 506_S | 2.268 | 1.00 |
| 60_M | 72_Y | 2.174 | 1.00 |
| 78_C | 81_D | 2.105 | 1.00 |
| 398_N | 401_D | 2.099 | 1.00 |
| 481_G | 557_F | 2.089 | 1.00 |
| 158_G | 255_Y | 2.058 | 1.00 |
| 72_Y | 78_C | 2.049 | 1.00 |
| 225_K | 520_D | 2.044 | 1.00 |
| 159_V | 211_V | 2.000 | 1.00 |
| 372_L | 376_I | 1.994 | 1.00 |
| 60_M | 64_W | 1.984 | 1.00 |
| 360_P | 364_N | 1.970 | 1.00 |
| 294_T | 297_Q | 1.939 | 1.00 |
| 225_K | 517_A | 1.910 | 1.00 |
| 64_W | 69_F | 1.898 | 1.00 |
| 438_R | 441_R | 1.896 | 1.00 |
| 392_Y | 402_F | 1.889 | 1.00 |
| 358_Q | 363_I | 1.831 | 1.00 |
| 218_L | 259_F | 1.825 | 1.00 |
| 327_I | 383_V | 1.822 | 1.00 |
| 155_S | 211_V | 1.813 | 1.00 |
| 224_F | 260_I | 1.792 | 1.00 |
| 336_F | 380_E | 1.782 | 0.99 |
| 561_Y | 565_S | 1.781 | 0.99 |
| 51_M | 55_V | 1.768 | 0.99 |
| 14_E | 21_I | 1.757 | 0.99 |
| 434_A | 438_R | 1.744 | 0.99 |
| 477_Y | 481_G | 1.737 | 0.99 |
| 293_M | 297_Q | 1.728 | 0.99 |
| 72_Y | 77_W | 1.717 | 0.99 |
| 169_C | 190_C | 1.713 | 0.99 |
| 77_W | 81_D | 1.710 | 0.99 |
| 297_Q | 300_Y | 1.705 | 0.99 |
| 392_Y | 398_N | 1.695 | 0.99 |
| 208_F | 256_F | 1.693 | 0.99 |
| 17_I | 21_I | 1.693 | 0.99 |
| 526_I | 558_F | 1.651 | 0.99 |
| 381_C | 384_K | 1.650 | 0.99 |
| 378_T | 409_I | 1.646 | 0.99 |
| 8_V | 62_L | 1.643 | 0.99 |
| 81_D | 85_V | 1.634 | 0.99 |
| 56_F | 59_E | 1.631 | 0.99 |
| 572_M | 581_F | 1.608 | 0.99 |
| 557_F | 561_Y | 1.608 | 0.99 |
| 17_I | 55_V | 1.605 | 0.99 |
| 336_F | 347_N | 1.597 | 0.99 |
| 293_M | 300_Y | 1.594 | 0.99 |
| 432_R | 436_I | 1.577 | 0.98 |
| 393_F | 399_I | 1.576 | 0.98 |
| 371_L | 375_A | 1.570 | 0.98 |
| 71_K | 74_T | 1.569 | 0.98 |
| 109_R | 112_R | 1.567 | 0.98 |
| 220_Q | 223_T | 1.567 | 0.98 |
| 72_Y | 82_F | 1.564 | 0.98 |
| 373_F | 380_E | 1.559 | 0.98 |
| 534_C | 548_C | 1.556 | 0.98 |
| 251_Y | 255_Y | 1.533 | 0.98 |
| 515_T | 519_W | 1.532 | 0.98 |
| 116_P | 122_R | 1.523 | 0.98 |
| 337_D | 344_I | 1.501 | 0.98 |
| 435_R | 438_R | 1.501 | 0.98 |
| 63_K | 72_Y | 1.500 | 0.98 |
| 340_I | 376_I | 1.497 | 0.98 |
| 359_S | 362_K | 1.482 | 0.97 |
| 498_F | 512_Q | 1.481 | 0.97 |
| 1_R | 4_C | 1.473 | 0.97 |
| 571_N | 575_A | 1.473 | 0.97 |
| 73_F | 82_F | 1.463 | 0.97 |
| 433_L | 436_I | 1.454 | 0.97 |
| 324_Q | 389_R | 1.450 | 0.97 |
| 69_F | 82_F | 1.444 | 0.97 |
| 327_I | 386_A | 1.444 | 0.97 |
| 487_Y | 501_Q | 1.435 | 0.97 |
| 347_N | 373_F | 1.434 | 0.97 |
| 353_V | 362_K | 1.434 | 0.97 |
| 392_Y | 401_D | 1.434 | 0.97 |
| 203_K | 209_D | 1.429 | 0.97 |
| 476_I | 483_A | 1.429 | 0.97 |
| 343_L | 377_F | 1.426 | 0.97 |
| 392_Y | 397_W | 1.424 | 0.97 |
| 108_L | 112_R | 1.414 | 0.96 |
| 164_G | 209_D | 1.414 | 0.96 |
| 245_Q | 248_Y | 1.414 | 0.96 |
| 384_K | 388_L | 1.412 | 0.96 |
| 385_L | 393_F | 1.412 | 0.96 |
| 576_I | 580_N | 1.408 | 0.96 |
| 158_G | 162_F | 1.404 | 0.96 |
| 608_D | 611_A | 1.402 | 0.96 |
| 60_M | 82_F | 1.397 | 0.96 |
| 380_E | 401_D | 1.394 | 0.96 |
| 162_F | 252_M | 1.393 | 0.96 |
| 429_R | 434_A | 1.388 | 0.96 |
| 354_E | 358_Q | 1.384 | 0.96 |
| 50_K | 54_Y | 1.382 | 0.96 |
| 115_R | 118_R | 1.382 | 0.96 |
| 330_I | 484_N | 1.379 | 0.96 |
| 325_G | 329_D | 1.377 | 0.96 |
| 510_L | 561_Y | 1.375 | 0.96 |
| 69_F | 73_F | 1.372 | 0.95 |
| 112_R | 116_P | 1.372 | 0.95 |
| 500_F | 506_S | 1.367 | 0.95 |
| 13_F | 17_I | 1.357 | 0.95 |
| 58_L | 62_L | 1.357 | 0.95 |
| 12_W | 15_T | 1.356 | 0.95 |
| 425_P | 429_R | 1.352 | 0.95 |
| 326_F | 330_I | 1.350 | 0.95 |
| 267_T | 274_V | 1.347 | 0.95 |
| 300_Y | 303_A | 1.346 | 0.95 |
| 478_S | 506_S | 1.338 | 0.95 |
| 525_P | 528_N | 1.337 | 0.95 |
| 438_R | 442_L | 1.331 | 0.94 |
| 440_L | 443_I | 1.324 | 0.94 |
| 571_N | 578_L | 1.317 | 0.94 |
| 126_M | 275_I | 1.306 | 0.94 |
| 235_V | 253_Y | 1.302 | 0.94 |
| 343_L | 376_I | 1.300 | 0.93 |
| 380_E | 387_A | 1.300 | 0.93 |
| 85_V | 88_S | 1.298 | 0.93 |
| 4_C | 65_V | 1.295 | 0.93 |
| 13_F | 21_I | 1.295 | 0.93 |
| 225_K | 228_M | 1.294 | 0.93 |
| 355_T | 359_S | 1.287 | 0.93 |
| 217_A | 230_I | 1.285 | 0.93 |
| 312_P | 319_P | 1.283 | 0.93 |
| 490_W | 501_Q | 1.266 | 0.92 |
| 517_A | 520_D | 1.261 | 0.92 |
| 478_S | 481_G | 1.254 | 0.92 |
| 63_K | 78_C | 1.253 | 0.92 |
| 109_R | 114_L | 1.252 | 0.92 |
| 340_I | 344_I | 1.250 | 0.92 |
| 523_L | 558_F | 1.249 | 0.92 |
| 70_K | 73_F | 1.247 | 0.91 |
| 73_F | 79_W | 1.245 | 0.91 |
| 519_W | 523_L | 1.238 | 0.91 |
| 159_V | 163_A | 1.237 | 0.91 |
| 502_T | 505_N | 1.236 | 0.91 |
| 59_E | 81_D | 1.231 | 0.91 |
| 427_L | 430_V | 1.228 | 0.91 |
| 429_R | 433_L | 1.228 | 0.91 |
| 63_K | 68_G | 1.223 | 0.90 |
| 558_F | 561_Y | 1.223 | 0.90 |
| 558_F | 565_S | 1.222 | 0.90 |
| 23_L | 27_A | 1.222 | 0.90 |
| 482_M | 485_F | 1.222 | 0.90 |
| 527_L | 555_I | 1.220 | 0.90 |
| 377_F | 408_S | 1.220 | 0.90 |
| 558_F | 566_F | 1.219 | 0.90 |
| 271_F | 278_N | 1.218 | 0.90 |
| 207_N | 213_A | 1.217 | 0.90 |
| 336_F | 340_I | 1.216 | 0.90 |
| 384_K | 392_Y | 1.212 | 0.90 |
| 296_E | 299_K | 1.211 | 0.90 |
| 554_G | 558_F | 1.210 | 0.90 |
| 25_S | 30_F | 1.210 | 0.90 |
| 384_K | 398_N | 1.207 | 0.90 |
| 482_M | 503_F | 1.206 | 0.90 |
| 318_R | 329_D | 1.205 | 0.90 |
| 498_F | 509_C | 1.199 | 0.89 |
| 5_Y | 9_E | 1.187 | 0.89 |
| 428_F | 432_R | 1.185 | 0.88 |
| 430_V | 438_R | 1.184 | 0.88 |
| 640_S | 666_R | 1.180 | 0.88 |
| 383_V | 387_A | 1.179 | 0.88 |
| 450_R | 453_L | 1.178 | 0.88 |
| 373_F | 377_F | 1.175 | 0.88 |
| 80_L | 85_V | 1.173 | 0.88 |
| 349_V | 353_V | 1.173 | 0.88 |
| 256_F | 265_F | 1.172 | 0.88 |
| 63_K | 81_D | 1.172 | 0.88 |
| 503_F | 507_M | 1.171 | 0.88 |
| 554_G | 557_F | 1.171 | 0.88 |
| 347_N | 351_M | 1.167 | 0.87 |
| 571_N | 581_F | 1.165 | 0.87 |
| 142_N | 146_V | 1.161 | 0.87 |
| 150_F | 153_I | 1.156 | 0.87 |
| 60_M | 63_K | 1.152 | 0.87 |
| 377_F | 384_K | 1.150 | 0.86 |
| 21_I | 28_L | 1.143 | 0.86 |
| 155_S | 214_G | 1.140 | 0.86 |
| 293_M | 298_K | 1.140 | 0.86 |
| 399_I | 403_V | 1.140 | 0.86 |
| 572_M | 578_L | 1.139 | 0.86 |
| 154_F | 158_G | 1.138 | 0.86 |
| 187_K | 191_E | 1.134 | 0.85 |
| 132_A | 136_A | 1.130 | 0.85 |
| 331_V | 387_A | 1.130 | 0.85 |
| 378_T | 405_V | 1.130 | 0.85 |
| 344_I | 348_M | 1.130 | 0.85 |
| 572_M | 577_I | 1.128 | 0.85 |
| 561_Y | 566_F | 1.127 | 0.85 |
| 59_E | 72_Y | 1.126 | 0.85 |
| 267_T | 273_G | 1.126 | 0.85 |
| 115_R | 120_L | 1.125 | 0.85 |
| 255_Y | 259_F | 1.118 | 0.84 |
| 374_V | 408_S | 1.116 | 0.84 |
| 572_M | 575_A | 1.115 | 0.84 |
| 10_H | 19_F | 1.111 | 0.84 |
| 443_I | 456_L | 1.110 | 0.84 |
| 593_S | 596_D | 1.109 | 0.84 |
| 355_T | 358_Q | 1.109 | 0.84 |
| 21_I | 24_S | 1.107 | 0.83 |
| 14_E | 28_L | 1.105 | 0.83 |
| 443_I | 446_A | 1.103 | 0.83 |
| 113_A | 118_R | 1.103 | 0.83 |
| 478_S | 483_A | 1.102 | 0.83 |
| 59_E | 66_A | 1.099 | 0.83 |
| 368_K | 372_L | 1.098 | 0.83 |
| 155_S | 215_Y | 1.095 | 0.83 |
| 348_M | 351_M | 1.094 | 0.82 |
| 214_G | 219_L | 1.094 | 0.82 |
| 575_A | 578_L | 1.094 | 0.82 |
| 435_R | 440_L | 1.094 | 0.82 |
| 88_S | 112_R | 1.093 | 0.82 |
| 368_K | 375_A | 1.092 | 0.82 |
| 344_I | 351_M | 1.091 | 0.82 |
| 384_K | 401_D | 1.087 | 0.82 |
| 440_L | 446_A | 1.086 | 0.82 |
| 332_T | 388_L | 1.084 | 0.82 |
| 52_F | 59_E | 1.084 | 0.82 |
| 426_T | 429_R | 1.082 | 0.81 |
| 370_N | 373_F | 1.080 | 0.81 |
| 171_N | 199_L | 1.079 | 0.81 |
| 295_E | 299_K | 1.076 | 0.81 |
| 482_M | 486_A | 1.075 | 0.81 |
| 616_E | 619_V | 1.074 | 0.81 |
| 270_L | 274_V | 1.074 | 0.81 |
| 59_E | 68_G | 1.070 | 0.80 |
| 116_P | 120_L | 1.069 | 0.80 |
| 297_Q | 301_Y | 1.064 | 0.80 |
| 295_E | 298_K | 1.062 | 0.80 |
| 269_N | 272_I | 1.061 | 0.80 |
| 209_D | 214_G | 1.060 | 0.80 |
| 342_F | 410_V | 1.059 | 0.80 |
| 113_A | 116_P | 1.058 | 0.79 |
| 178_P | 181_Y | 1.055 | 0.79 |
| 369_I | 373_F | 1.055 | 0.79 |
| 212_G | 478_S | 1.053 | 0.79 |
| 658_D | 664_T | 1.053 | 0.79 |
| 566_F | 570_V | 1.051 | 0.79 |
| 500_F | 510_L | 1.050 | 0.79 |
| 220_Q | 524_S | 1.049 | 0.79 |
| 351_M | 370_N | 1.048 | 0.79 |
| 430_V | 434_A | 1.046 | 0.78 |
| 253_Y | 257_V | 1.045 | 0.78 |
| 344_I | 347_N | 1.044 | 0.78 |
| 130_V | 133_L | 1.043 | 0.78 |
| 381_C | 385_L | 1.042 | 0.78 |
| 575_A | 580_N | 1.042 | 0.78 |
| 481_G | 484_N | 1.040 | 0.78 |
| 210_N | 213_A | 1.039 | 0.78 |
| 76_A | 79_W | 1.038 | 0.78 |
| 604_W | 608_D | 1.036 | 0.77 |
| 474_M | 510_L | 1.035 | 0.77 |
| 225_K | 231_M | 1.034 | 0.77 |
| 606_K | 626_A | 1.030 | 0.77 |
| 397_W | 405_V | 1.030 | 0.77 |
| 25_S | 49_D | 1.029 | 0.77 |
| 293_M | 296_E | 1.029 | 0.77 |
| 13_F | 59_E | 1.028 | 0.77 |
| 291_I | 294_T | 1.027 | 0.77 |
| 25_S | 28_L | 1.027 | 0.77 |
| 512_Q | 522_L | 1.027 | 0.77 |
| 481_G | 500_F | 1.026 | 0.76 |
| 434_A | 437_G | 1.025 | 0.76 |
| 90_V | 379_G | 1.023 | 0.76 |
| 330_I | 383_V | 1.023 | 0.76 |
| 53_T | 88_S | 1.023 | 0.76 |
| 64_W | 73_F | 1.022 | 0.76 |
| 33_I | 38_R | 1.021 | 0.76 |
| 573_Y | 580_N | 1.020 | 0.76 |
| 61_L | 65_V | 1.019 | 0.76 |
| 339_T | 342_F | 1.019 | 0.76 |
| 347_N | 370_N | 1.018 | 0.76 |
| 166_F | 169_C | 1.018 | 0.76 |
| 375_A | 379_G | 1.018 | 0.76 |
| 146_V | 151_W | 1.017 | 0.76 |
| 577_I | 580_N | 1.013 | 0.75 |
| 21_I | 25_S | 1.012 | 0.75 |
| 296_E | 300_Y | 1.010 | 0.75 |
| 398_N | 404_V | 1.010 | 0.75 |
| 49_D | 56_F | 1.008 | 0.75 |
| 377_F | 380_E | 1.007 | 0.75 |
| 72_Y | 85_V | 1.006 | 0.74 |
| 120_L | 126_M | 1.006 | 0.74 |
| 661_F | 664_T | 1.005 | 0.74 |
| 649_V | 652_D | 1.003 | 0.74 |
| 227_W | 517_A | 1.003 | 0.74 |
| 292_F | 297_Q | 1.000 | 0.74 |
| 219_L | 225_K | 1.000 | 0.74 |
| 608_D | 615_I | 1.000 | 0.74 |
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 | |
| 4dxwA | 4 | 0.2689 | 100 | 0.805 | Contact Map |
| 3rvyA | 2 | 0.2664 | 100 | 0.811 | Contact Map |
| 4bgnA | 2 | 0.2603 | 100 | 0.815 | Contact Map |
| 4jpzB | 2 | 0.1727 | 100 | 0.827 | Contact Map |
| 4dckA | 1 | 0.1861 | 100 | 0.843 | Contact Map |
| 3j9pD | 4 | 0.6095 | 100 | 0.845 | Contact Map |
| 2r9rB | 2 | 0.4148 | 100 | 0.847 | Contact Map |
| 3behA | 4 | 0.2713 | 100 | 0.849 | Contact Map |
| 4cbcA | 4 | 0.1119 | 99.9 | 0.873 | Contact Map |
| 4ltoA | 4 | 0.1667 | 99.9 | 0.874 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)