| HARS2 repeat |
| ID: | 1509570761 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 506 (438) | ||
| Sequences: | 12651 (5837.3) | ||
| Seq/Len: | 28.884 | ||
| Nf(neff/√len): | 278.9 |
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: 28.884).
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 |
| 211_K | 322_D | 3.285 | 1.00 |
| 152_H | 176_D | 3.060 | 1.00 |
| 334_G | 355_V | 2.834 | 1.00 |
| 414_V | 429_I | 2.578 | 1.00 |
| 101_K | 105_T | 2.504 | 1.00 |
| 285_F | 304_K | 2.491 | 1.00 |
| 424_E | 427_K | 2.490 | 1.00 |
| 79_D | 83_S | 2.469 | 1.00 |
| 82_I | 92_G | 2.443 | 1.00 |
| 469_E | 473_K | 2.443 | 1.00 |
| 102_E | 105_T | 2.413 | 1.00 |
| 470_Q | 473_K | 2.375 | 1.00 |
| 311_T | 319_I | 2.375 | 1.00 |
| 429_I | 439_A | 2.344 | 1.00 |
| 75_E | 92_G | 2.317 | 1.00 |
| 470_Q | 474_E | 2.311 | 1.00 |
| 80_L | 202_G | 2.213 | 1.00 |
| 93_M | 139_Y | 2.195 | 1.00 |
| 63_T | 98_F | 2.127 | 1.00 |
| 429_I | 441_M | 2.126 | 1.00 |
| 427_K | 431_E | 2.120 | 1.00 |
| 88_H | 198_E | 2.108 | 1.00 |
| 427_K | 475_G | 2.102 | 1.00 |
| 85_F | 175_C | 2.089 | 1.00 |
| 81_V | 199_I | 2.056 | 1.00 |
| 101_K | 125_L | 2.039 | 1.00 |
| 97_A | 157_W | 2.013 | 1.00 |
| 84_C | 87_R | 2.000 | 1.00 |
| 491_K | 494_N | 1.988 | 1.00 |
| 155_K | 171_E | 1.988 | 1.00 |
| 421_F | 469_E | 1.949 | 1.00 |
| 220_G | 296_A | 1.944 | 1.00 |
| 75_E | 82_I | 1.932 | 1.00 |
| 481_S | 484_S | 1.927 | 1.00 |
| 84_C | 198_E | 1.924 | 1.00 |
| 464_V | 482_V | 1.919 | 1.00 |
| 190_A | 309_Y | 1.878 | 1.00 |
| 494_N | 497_A | 1.852 | 1.00 |
| 196_M | 339_A | 1.817 | 1.00 |
| 476_V | 491_K | 1.790 | 1.00 |
| 410_T | 440_E | 1.780 | 1.00 |
| 83_S | 202_G | 1.775 | 1.00 |
| 84_C | 202_G | 1.750 | 1.00 |
| 78_L | 94_D | 1.743 | 1.00 |
| 84_C | 88_H | 1.742 | 1.00 |
| 444_K | 455_Y | 1.732 | 1.00 |
| 75_E | 86_K | 1.732 | 1.00 |
| 412_V | 465_V | 1.730 | 1.00 |
| 395_E | 402_G | 1.710 | 1.00 |
| 75_E | 79_D | 1.709 | 1.00 |
| 220_G | 299_G | 1.699 | 1.00 |
| 296_A | 299_G | 1.681 | 1.00 |
| 468_G | 471_E | 1.669 | 1.00 |
| 431_E | 493_E | 1.662 | 1.00 |
| 412_V | 437_I | 1.661 | 1.00 |
| 414_V | 425_R | 1.658 | 1.00 |
| 479_I | 498_E | 1.655 | 1.00 |
| 75_E | 78_L | 1.634 | 1.00 |
| 453_L | 466_I | 1.628 | 1.00 |
| 418_Q | 469_E | 1.625 | 1.00 |
| 196_M | 359_A | 1.623 | 1.00 |
| 177_F | 195_I | 1.623 | 1.00 |
| 429_I | 433_W | 1.615 | 1.00 |
| 217_I | 296_A | 1.609 | 1.00 |
| 189_D | 237_S | 1.607 | 1.00 |
| 101_K | 127_S | 1.598 | 1.00 |
| 99_E | 135_P | 1.591 | 1.00 |
| 415_A | 449_L | 1.584 | 1.00 |
| 498_E | 502_R | 1.584 | 1.00 |
| 411_Q | 438_K | 1.582 | 1.00 |
| 431_E | 492_R | 1.570 | 1.00 |
| 76_K | 80_L | 1.569 | 1.00 |
| 478_K | 487_E | 1.562 | 1.00 |
| 81_V | 85_F | 1.561 | 1.00 |
| 161_S | 164_I | 1.560 | 1.00 |
| 209_L | 320_S | 1.545 | 1.00 |
| 303_L | 321_F | 1.521 | 1.00 |
| 428_L | 492_R | 1.517 | 1.00 |
| 72_V | 91_K | 1.513 | 1.00 |
| 119_K | 123_G | 1.511 | 1.00 |
| 416_T | 452_Q | 1.488 | 1.00 |
| 71_M | 94_D | 1.485 | 1.00 |
| 60_P | 63_T | 1.484 | 1.00 |
| 86_K | 151_Y | 1.480 | 1.00 |
| 60_P | 98_F | 1.469 | 1.00 |
| 128_L | 157_W | 1.463 | 1.00 |
| 444_K | 447_P | 1.459 | 1.00 |
| 60_P | 126_L | 1.426 | 1.00 |
| 479_I | 495_F | 1.422 | 1.00 |
| 189_D | 241_K | 1.421 | 1.00 |
| 179_I | 188_P | 1.419 | 1.00 |
| 194_K | 198_E | 1.414 | 1.00 |
| 327_R | 356_G | 1.408 | 1.00 |
| 497_A | 501_K | 1.397 | 0.99 |
| 481_S | 502_R | 1.380 | 0.99 |
| 457_E | 464_V | 1.379 | 0.99 |
| 448_K | 451_T | 1.374 | 0.99 |
| 413_F | 456_C | 1.374 | 0.99 |
| 330_D | 356_G | 1.363 | 0.99 |
| 369_G | 377_K | 1.355 | 0.99 |
| 74_R | 94_D | 1.355 | 0.99 |
| 334_G | 343_Q | 1.354 | 0.99 |
| 416_T | 425_R | 1.346 | 0.99 |
| 197_C | 201_S | 1.336 | 0.99 |
| 149_K | 440_E | 1.328 | 0.99 |
| 70_H | 395_E | 1.327 | 0.99 |
| 149_K | 191_E | 1.326 | 0.99 |
| 117_D | 127_S | 1.324 | 0.99 |
| 78_L | 82_I | 1.324 | 0.99 |
| 132_L | 176_D | 1.317 | 0.99 |
| 73_V | 395_E | 1.312 | 0.99 |
| 95_T | 135_P | 1.309 | 0.99 |
| 359_A | 385_I | 1.307 | 0.99 |
| 197_C | 210_I | 1.298 | 0.99 |
| 307_F | 311_T | 1.295 | 0.99 |
| 137_A | 180_A | 1.289 | 0.99 |
| 83_S | 87_R | 1.285 | 0.99 |
| 414_V | 428_L | 1.283 | 0.99 |
| 97_A | 154_G | 1.274 | 0.99 |
| 132_L | 156_V | 1.271 | 0.99 |
| 307_F | 319_I | 1.271 | 0.99 |
| 173_C | 388_E | 1.269 | 0.99 |
| 97_A | 171_E | 1.266 | 0.99 |
| 301_G | 305_L | 1.263 | 0.99 |
| 456_C | 464_V | 1.263 | 0.99 |
| 495_F | 499_I | 1.263 | 0.99 |
| 87_R | 202_G | 1.261 | 0.99 |
| 97_A | 155_K | 1.256 | 0.99 |
| 343_Q | 355_V | 1.255 | 0.99 |
| 61_K | 161_S | 1.252 | 0.99 |
| 422_L | 469_E | 1.250 | 0.99 |
| 73_V | 391_F | 1.247 | 0.99 |
| 101_K | 117_D | 1.245 | 0.98 |
| 79_D | 82_I | 1.240 | 0.98 |
| 129_R | 154_G | 1.239 | 0.98 |
| 117_D | 125_L | 1.238 | 0.98 |
| 211_K | 320_S | 1.232 | 0.98 |
| 72_V | 76_K | 1.231 | 0.98 |
| 137_A | 368_V | 1.231 | 0.98 |
| 457_E | 480_R | 1.229 | 0.98 |
| 420_N | 469_E | 1.226 | 0.98 |
| 137_A | 367_L | 1.222 | 0.98 |
| 498_E | 501_K | 1.220 | 0.98 |
| 475_G | 493_E | 1.220 | 0.98 |
| 198_E | 202_G | 1.214 | 0.98 |
| 297_L | 301_G | 1.205 | 0.98 |
| 430_A | 434_D | 1.200 | 0.98 |
| 179_I | 192_C | 1.200 | 0.98 |
| 76_K | 79_D | 1.196 | 0.98 |
| 424_E | 428_L | 1.190 | 0.98 |
| 236_C | 240_D | 1.189 | 0.98 |
| 71_M | 92_G | 1.188 | 0.98 |
| 160_E | 168_R | 1.187 | 0.98 |
| 437_I | 499_I | 1.186 | 0.98 |
| 307_F | 321_F | 1.182 | 0.98 |
| 426_L | 429_I | 1.180 | 0.98 |
| 136_F | 180_A | 1.173 | 0.98 |
| 91_K | 440_E | 1.173 | 0.98 |
| 453_L | 457_E | 1.171 | 0.98 |
| 339_A | 359_A | 1.171 | 0.98 |
| 155_K | 173_C | 1.166 | 0.97 |
| 500_Q | 504_S | 1.166 | 0.97 |
| 99_E | 138_R | 1.164 | 0.97 |
| 77_I | 391_F | 1.163 | 0.97 |
| 132_L | 152_H | 1.162 | 0.97 |
| 465_V | 495_F | 1.161 | 0.97 |
| 415_A | 464_V | 1.160 | 0.97 |
| 93_M | 136_F | 1.159 | 0.97 |
| 465_V | 477_I | 1.159 | 0.97 |
| 431_E | 434_D | 1.158 | 0.97 |
| 197_C | 208_F | 1.158 | 0.97 |
| 92_G | 151_Y | 1.157 | 0.97 |
| 369_G | 376_H | 1.157 | 0.97 |
| 98_F | 126_L | 1.157 | 0.97 |
| 404_K | 502_R | 1.153 | 0.97 |
| 119_K | 125_L | 1.153 | 0.97 |
| 217_I | 220_G | 1.151 | 0.97 |
| 428_L | 431_E | 1.149 | 0.97 |
| 200_L | 390_I | 1.141 | 0.97 |
| 424_E | 472_L | 1.141 | 0.97 |
| 497_A | 500_Q | 1.139 | 0.97 |
| 496_V | 500_Q | 1.135 | 0.97 |
| 175_C | 387_V | 1.134 | 0.97 |
| 490_I | 498_E | 1.134 | 0.97 |
| 304_K | 308_E | 1.133 | 0.97 |
| 246_A | 254_M | 1.133 | 0.97 |
| 424_E | 467_I | 1.130 | 0.97 |
| 254_M | 274_C | 1.128 | 0.97 |
| 120_D | 123_G | 1.127 | 0.97 |
| 217_I | 299_G | 1.127 | 0.97 |
| 153_V | 175_C | 1.125 | 0.97 |
| 157_W | 171_E | 1.124 | 0.97 |
| 451_T | 455_Y | 1.123 | 0.97 |
| 442_L | 452_Q | 1.122 | 0.97 |
| 476_V | 489_A | 1.119 | 0.96 |
| 88_H | 195_I | 1.112 | 0.96 |
| 72_V | 86_K | 1.111 | 0.96 |
| 417_P | 449_L | 1.110 | 0.96 |
| 501_K | 504_S | 1.109 | 0.96 |
| 465_V | 479_I | 1.105 | 0.96 |
| 413_F | 459_T | 1.103 | 0.96 |
| 196_M | 383_L | 1.097 | 0.96 |
| 431_E | 496_V | 1.093 | 0.96 |
| 282_E | 304_K | 1.092 | 0.96 |
| 69_Q | 459_T | 1.087 | 0.96 |
| 488_V | 498_E | 1.087 | 0.96 |
| 426_L | 441_M | 1.085 | 0.96 |
| 305_L | 309_Y | 1.084 | 0.96 |
| 386_G | 389_R | 1.083 | 0.96 |
| 226_G | 268_I | 1.081 | 0.95 |
| 455_Y | 459_T | 1.078 | 0.95 |
| 192_C | 381_V | 1.077 | 0.95 |
| 80_L | 84_C | 1.076 | 0.95 |
| 463_L | 502_R | 1.072 | 0.95 |
| 451_T | 454_H | 1.072 | 0.95 |
| 256_V | 260_L | 1.071 | 0.95 |
| 198_E | 430_A | 1.071 | 0.95 |
| 73_V | 76_K | 1.067 | 0.95 |
| 285_F | 301_G | 1.064 | 0.95 |
| 283_Q | 286_Q | 1.062 | 0.95 |
| 211_K | 340_V | 1.061 | 0.95 |
| 66_L | 391_F | 1.055 | 0.95 |
| 90_A | 179_I | 1.054 | 0.95 |
| 308_E | 423_Q | 1.053 | 0.95 |
| 413_F | 461_I | 1.051 | 0.94 |
| 233_R | 236_C | 1.051 | 0.94 |
| 78_L | 387_V | 1.048 | 0.94 |
| 136_F | 176_D | 1.047 | 0.94 |
| 152_H | 156_V | 1.047 | 0.94 |
| 172_F | 386_G | 1.046 | 0.94 |
| 77_I | 203_L | 1.039 | 0.94 |
| 118_L | 126_L | 1.038 | 0.94 |
| 274_C | 277_G | 1.037 | 0.94 |
| 431_E | 435_S | 1.037 | 0.94 |
| 426_L | 443_Y | 1.028 | 0.94 |
| 100_L | 124_E | 1.027 | 0.94 |
| 94_D | 155_K | 1.025 | 0.93 |
| 414_V | 465_V | 1.024 | 0.93 |
| 74_R | 78_L | 1.023 | 0.93 |
| 81_V | 175_C | 1.018 | 0.93 |
| 67_S | 139_Y | 1.016 | 0.93 |
| 435_S | 500_Q | 1.013 | 0.93 |
| 334_G | 345_P | 1.012 | 0.93 |
| 64_R | 388_E | 1.009 | 0.93 |
| 494_N | 498_E | 1.006 | 0.93 |
| 224_V | 228_P | 1.006 | 0.93 |
| 474_E | 489_A | 1.005 | 0.93 |
| 69_Q | 440_E | 1.003 | 0.93 |
| 298_E | 301_G | 1.002 | 0.92 |
| 85_F | 177_F | 1.002 | 0.92 |
| 84_C | 199_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
- 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 | |
| 4phcA | 4 | 0.8874 | 100 | 0.221 | Contact Map |
| 4g84A | 2 | 0.8814 | 100 | 0.258 | Contact Map |
| 3netA | 2 | 0.832 | 100 | 0.297 | Contact Map |
| 1wu7A | 2 | 0.8241 | 100 | 0.305 | Contact Map |
| 3lc0A | 1 | 0.8083 | 100 | 0.308 | Contact Map |
| 3od1A | 2 | 0.751 | 100 | 0.335 | Contact Map |
| 1httA | 4 | 0.7036 | 100 | 0.351 | Contact Map |
| 1h4vB | 1 | 0.7767 | 100 | 0.358 | Contact Map |
| 1qe0A | 2 | 0.7589 | 100 | 0.375 | Contact Map |
| 4e51A | 2 | 0.8004 | 100 | 0.383 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)