| Ankur Dalia |
| ID: | 1466715364 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 507 (472) | ||
| Sequences: | 3003 (1873.2) | ||
| Seq/Len: | 6.362 | ||
| Nf(neff/√len): | 86.2 |
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: 6.362).
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 |
| 191_L | 407_V | 4.801 | 1.00 |
| 205_E | 410_R | 4.464 | 1.00 |
| 422_S | 429_L | 3.964 | 1.00 |
| 441_L | 444_D | 3.892 | 1.00 |
| 322_G | 338_R | 3.774 | 1.00 |
| 116_I | 157_A | 3.555 | 1.00 |
| 202_R | 488_E | 3.550 | 1.00 |
| 246_T | 296_N | 3.453 | 1.00 |
| 126_A | 136_L | 3.382 | 1.00 |
| 140_H | 158_Q | 3.360 | 1.00 |
| 157_A | 163_V | 3.187 | 1.00 |
| 205_E | 407_V | 3.159 | 1.00 |
| 402_E | 410_R | 3.156 | 1.00 |
| 478_E | 485_H | 3.139 | 1.00 |
| 323_E | 334_R | 3.030 | 1.00 |
| 403_S | 406_A | 3.025 | 1.00 |
| 106_F | 137_V | 2.931 | 1.00 |
| 402_E | 407_V | 2.914 | 1.00 |
| 32_F | 67_V | 2.868 | 1.00 |
| 205_E | 402_E | 2.797 | 1.00 |
| 268_R | 290_E | 2.747 | 1.00 |
| 158_Q | 162_E | 2.737 | 1.00 |
| 274_S | 278_A | 2.722 | 1.00 |
| 237_E | 412_W | 2.712 | 1.00 |
| 226_M | 230_R | 2.648 | 1.00 |
| 231_L | 342_V | 2.606 | 1.00 |
| 451_A | 490_L | 2.601 | 1.00 |
| 382_M | 468_V | 2.552 | 1.00 |
| 407_V | 410_R | 2.458 | 1.00 |
| 296_N | 428_L | 2.443 | 1.00 |
| 312_L | 376_L | 2.418 | 1.00 |
| 24_H | 55_N | 2.349 | 1.00 |
| 476_Q | 485_H | 2.346 | 1.00 |
| 206_I | 472_I | 2.332 | 1.00 |
| 87_L | 106_F | 2.311 | 1.00 |
| 247_A | 262_W | 2.291 | 1.00 |
| 209_A | 475_L | 2.280 | 1.00 |
| 234_L | 404_T | 2.251 | 1.00 |
| 348_S | 358_A | 2.247 | 1.00 |
| 204_L | 231_L | 2.222 | 1.00 |
| 304_M | 343_G | 2.218 | 1.00 |
| 279_L | 311_V | 2.193 | 1.00 |
| 348_S | 360_A | 2.186 | 1.00 |
| 204_L | 227_L | 2.176 | 1.00 |
| 193_D | 230_R | 2.129 | 1.00 |
| 189_R | 233_D | 2.119 | 1.00 |
| 40_T | 43_K | 2.112 | 1.00 |
| 23_V | 84_P | 2.112 | 1.00 |
| 211_N | 425_V | 2.091 | 1.00 |
| 361_N | 364_S | 2.088 | 1.00 |
| 194_I | 230_R | 2.082 | 1.00 |
| 273_S | 314_S | 2.074 | 1.00 |
| 408_R | 412_W | 2.069 | 1.00 |
| 353_Y | 388_A | 2.063 | 1.00 |
| 414_A | 475_L | 2.041 | 1.00 |
| 286_P | 335_F | 2.034 | 1.00 |
| 91_A | 101_L | 2.014 | 1.00 |
| 137_V | 163_V | 2.013 | 1.00 |
| 416_E | 420_A | 1.996 | 1.00 |
| 108_G | 139_P | 1.995 | 1.00 |
| 444_D | 486_L | 1.965 | 1.00 |
| 206_I | 382_M | 1.945 | 1.00 |
| 242_E | 265_R | 1.941 | 1.00 |
| 350_T | 358_A | 1.933 | 1.00 |
| 305_P | 345_L | 1.925 | 1.00 |
| 200_G | 227_L | 1.913 | 1.00 |
| 214_L | 342_V | 1.895 | 1.00 |
| 143_G | 147_A | 1.892 | 1.00 |
| 143_G | 156_S | 1.886 | 1.00 |
| 406_A | 409_Q | 1.834 | 1.00 |
| 424_K | 433_E | 1.819 | 1.00 |
| 107_I | 125_A | 1.812 | 1.00 |
| 420_A | 423_G | 1.812 | 1.00 |
| 104_Y | 137_V | 1.809 | 1.00 |
| 392_G | 449_E | 1.778 | 1.00 |
| 233_D | 404_T | 1.778 | 1.00 |
| 274_S | 279_L | 1.756 | 1.00 |
| 211_N | 427_A | 1.749 | 1.00 |
| 188_T | 233_D | 1.742 | 1.00 |
| 435_E | 463_H | 1.739 | 1.00 |
| 434_I | 467_K | 1.712 | 1.00 |
| 229_S | 321_S | 1.708 | 1.00 |
| 476_Q | 484_P | 1.695 | 1.00 |
| 238_M | 246_T | 1.673 | 1.00 |
| 447_F | 487_A | 1.668 | 1.00 |
| 482_A | 485_H | 1.665 | 1.00 |
| 465_I | 490_L | 1.665 | 1.00 |
| 304_M | 376_L | 1.662 | 1.00 |
| 211_N | 415_R | 1.656 | 1.00 |
| 350_T | 360_A | 1.648 | 1.00 |
| 122_V | 138_V | 1.646 | 1.00 |
| 209_A | 414_A | 1.642 | 1.00 |
| 430_Q | 433_E | 1.633 | 1.00 |
| 238_M | 265_R | 1.626 | 1.00 |
| 208_A | 235_L | 1.624 | 1.00 |
| 338_R | 428_L | 1.616 | 1.00 |
| 325_V | 334_R | 1.613 | 1.00 |
| 478_E | 482_A | 1.609 | 1.00 |
| 300_F | 344_A | 1.569 | 0.99 |
| 86_A | 160_L | 1.555 | 0.99 |
| 191_L | 214_L | 1.551 | 0.99 |
| 291_I | 324_I | 1.541 | 0.99 |
| 304_M | 312_L | 1.535 | 0.99 |
| 208_A | 231_L | 1.535 | 0.99 |
| 389_L | 393_T | 1.526 | 0.99 |
| 204_L | 214_L | 1.522 | 0.99 |
| 87_L | 163_V | 1.519 | 0.99 |
| 280_V | 324_I | 1.519 | 0.99 |
| 440_L | 444_D | 1.516 | 0.99 |
| 412_W | 416_E | 1.500 | 0.99 |
| 24_H | 54_I | 1.490 | 0.99 |
| 155_K | 166_D | 1.452 | 0.99 |
| 106_F | 116_I | 1.446 | 0.99 |
| 161_L | 165_A | 1.441 | 0.99 |
| 239_S | 242_E | 1.436 | 0.99 |
| 138_V | 154_H | 1.431 | 0.99 |
| 225_T | 321_S | 1.420 | 0.99 |
| 215_L | 345_L | 1.412 | 0.99 |
| 30_P | 50_R | 1.411 | 0.99 |
| 190_D | 404_T | 1.410 | 0.99 |
| 191_L | 234_L | 1.399 | 0.98 |
| 159_S | 162_E | 1.386 | 0.98 |
| 364_S | 367_R | 1.382 | 0.98 |
| 201_K | 402_E | 1.378 | 0.98 |
| 242_E | 296_N | 1.377 | 0.98 |
| 60_F | 89_I | 1.375 | 0.98 |
| 416_E | 419_L | 1.373 | 0.98 |
| 431_S | 463_H | 1.372 | 0.98 |
| 413_V | 477_G | 1.370 | 0.98 |
| 438_C | 481_I | 1.366 | 0.98 |
| 124_P | 252_L | 1.358 | 0.98 |
| 237_E | 408_R | 1.352 | 0.98 |
| 189_R | 230_R | 1.345 | 0.98 |
| 193_D | 226_M | 1.345 | 0.98 |
| 247_A | 261_N | 1.339 | 0.98 |
| 308_E | 311_V | 1.337 | 0.98 |
| 415_R | 425_V | 1.334 | 0.98 |
| 53_I | 60_F | 1.331 | 0.98 |
| 296_N | 338_R | 1.327 | 0.98 |
| 390_P | 393_T | 1.314 | 0.97 |
| 115_E | 159_S | 1.305 | 0.97 |
| 198_Q | 393_T | 1.303 | 0.97 |
| 305_P | 372_L | 1.300 | 0.97 |
| 140_H | 162_E | 1.292 | 0.97 |
| 441_L | 482_A | 1.288 | 0.97 |
| 187_Q | 233_D | 1.285 | 0.97 |
| 301_L | 341_L | 1.278 | 0.97 |
| 119_V | 122_V | 1.272 | 0.97 |
| 488_E | 492_Y | 1.256 | 0.96 |
| 107_I | 119_V | 1.253 | 0.96 |
| 458_S | 461_A | 1.252 | 0.96 |
| 129_A | 136_L | 1.251 | 0.96 |
| 230_R | 233_D | 1.250 | 0.96 |
| 434_I | 438_C | 1.244 | 0.96 |
| 245_E | 296_N | 1.244 | 0.96 |
| 50_R | 60_F | 1.239 | 0.96 |
| 313_D | 373_S | 1.238 | 0.96 |
| 137_V | 166_D | 1.238 | 0.96 |
| 443_A | 483_R | 1.236 | 0.96 |
| 209_A | 471_T | 1.232 | 0.96 |
| 122_V | 126_A | 1.211 | 0.95 |
| 268_R | 293_L | 1.192 | 0.95 |
| 200_G | 386_I | 1.192 | 0.95 |
| 363_Q | 367_R | 1.183 | 0.94 |
| 198_Q | 201_K | 1.181 | 0.94 |
| 165_A | 170_Q | 1.179 | 0.94 |
| 405_A | 409_Q | 1.167 | 0.94 |
| 247_A | 250_A | 1.165 | 0.94 |
| 126_A | 152_E | 1.161 | 0.94 |
| 23_V | 69_L | 1.154 | 0.93 |
| 145_Q | 251_S | 1.146 | 0.93 |
| 69_L | 85_I | 1.143 | 0.93 |
| 225_T | 229_S | 1.141 | 0.93 |
| 413_V | 416_E | 1.135 | 0.93 |
| 110_L | 160_L | 1.135 | 0.93 |
| 231_L | 340_Q | 1.134 | 0.93 |
| 380_F | 383_S | 1.131 | 0.92 |
| 190_D | 234_L | 1.127 | 0.92 |
| 32_F | 60_F | 1.125 | 0.92 |
| 116_I | 163_V | 1.124 | 0.92 |
| 353_Y | 356_S | 1.120 | 0.92 |
| 431_S | 434_I | 1.119 | 0.92 |
| 445_A | 449_E | 1.109 | 0.91 |
| 237_E | 264_L | 1.108 | 0.91 |
| 413_V | 417_R | 1.108 | 0.91 |
| 442_K | 446_E | 1.107 | 0.91 |
| 243_A | 262_W | 1.100 | 0.91 |
| 417_R | 477_G | 1.099 | 0.91 |
| 47_D | 50_R | 1.097 | 0.91 |
| 208_A | 411_V | 1.096 | 0.91 |
| 449_E | 453_H | 1.092 | 0.91 |
| 96_I | 168_C | 1.090 | 0.91 |
| 118_G | 142_N | 1.084 | 0.90 |
| 309_R | 313_D | 1.084 | 0.90 |
| 327_S | 332_K | 1.080 | 0.90 |
| 25_I | 93_S | 1.080 | 0.90 |
| 111_A | 117_R | 1.079 | 0.90 |
| 107_I | 122_V | 1.079 | 0.90 |
| 440_L | 486_L | 1.078 | 0.90 |
| 211_N | 340_Q | 1.077 | 0.90 |
| 104_Y | 166_D | 1.076 | 0.90 |
| 291_I | 339_F | 1.075 | 0.90 |
| 450_S | 454_R | 1.069 | 0.89 |
| 67_V | 85_I | 1.064 | 0.89 |
| 106_F | 163_V | 1.062 | 0.89 |
| 70_A | 117_R | 1.062 | 0.89 |
| 137_V | 157_A | 1.060 | 0.89 |
| 216_F | 384_I | 1.059 | 0.89 |
| 143_G | 154_H | 1.051 | 0.88 |
| 91_A | 96_I | 1.046 | 0.88 |
| 277_A | 329_A | 1.046 | 0.88 |
| 163_V | 166_D | 1.044 | 0.88 |
| 22_E | 115_E | 1.023 | 0.86 |
| 124_P | 248_S | 1.021 | 0.86 |
| 425_V | 428_L | 1.019 | 0.86 |
| 234_L | 411_V | 1.017 | 0.86 |
| 215_L | 377_L | 1.011 | 0.86 |
| 106_F | 167_L | 1.010 | 0.85 |
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 | |
| 3ja82 | 1 | 0 | 100 | 0.801 | Contact Map |
| 2x36A | 6 | 0.3373 | 100 | 0.81 | Contact Map |
| 3wu4A | 6 | 0.3531 | 100 | 0.812 | Contact Map |
| 4r7yA | 2 | 0.8462 | 100 | 0.813 | Contact Map |
| 1z0wA | 1 | 0.3688 | 100 | 0.816 | Contact Map |
| 1xhkA | 2 | 0.3333 | 100 | 0.817 | Contact Map |
| 1g8pA | 1 | 0.5444 | 100 | 0.818 | Contact Map |
| 3ja84 | 1 | 0 | 100 | 0.821 | Contact Map |
| 3m6aA | 6 | 0.3294 | 100 | 0.822 | Contact Map |
| 3ja87 | 1 | 0 | 100 | 0.825 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)