| Lisa N Kinch |
| ID: | 1483639200 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 485 (417) | ||
| Sequences: | 2101 (1006.5) | ||
| Seq/Len: | 5.038 | ||
| Nf(neff/√len): | 49.3 |
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: 5.038).
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 |
| 355_Q | 373_K | 3.743 | 1.00 |
| 383_V | 441_V | 3.691 | 1.00 |
| 137_P | 140_P | 3.278 | 1.00 |
| 398_V | 401_G | 3.083 | 1.00 |
| 68_A | 356_L | 3.034 | 1.00 |
| 115_W | 127_P | 3.009 | 1.00 |
| 398_V | 447_T | 2.936 | 1.00 |
| 241_W | 251_W | 2.671 | 1.00 |
| 140_P | 146_R | 2.638 | 1.00 |
| 291_Y | 352_D | 2.602 | 1.00 |
| 446_T | 450_N | 2.590 | 1.00 |
| 196_C | 208_L | 2.584 | 1.00 |
| 159_D | 162_L | 2.579 | 1.00 |
| 389_R | 445_E | 2.554 | 1.00 |
| 312_L | 316_P | 2.533 | 1.00 |
| 204_L | 331_V | 2.455 | 1.00 |
| 119_V | 209_A | 2.423 | 1.00 |
| 443_V | 447_T | 2.282 | 1.00 |
| 402_L | 443_V | 2.263 | 1.00 |
| 259_R | 301_E | 2.234 | 1.00 |
| 99_F | 343_D | 2.223 | 1.00 |
| 130_A | 188_G | 2.214 | 1.00 |
| 272_N | 292_N | 2.205 | 1.00 |
| 134_K | 191_E | 2.180 | 1.00 |
| 76_R | 434_E | 2.176 | 1.00 |
| 190_L | 240_V | 2.172 | 1.00 |
| 189_A | 339_N | 2.161 | 1.00 |
| 150_A | 159_D | 2.105 | 1.00 |
| 313_H | 316_P | 2.089 | 1.00 |
| 173_N | 183_E | 2.088 | 1.00 |
| 455_L | 474_F | 2.053 | 1.00 |
| 457_S | 460_T | 1.999 | 1.00 |
| 108_K | 112_A | 1.958 | 1.00 |
| 150_A | 162_L | 1.956 | 1.00 |
| 277_D | 287_N | 1.953 | 1.00 |
| 109_N | 382_K | 1.942 | 1.00 |
| 357_T | 461_T | 1.893 | 1.00 |
| 240_V | 304_W | 1.879 | 1.00 |
| 470_K | 473_D | 1.877 | 1.00 |
| 277_D | 285_K | 1.874 | 1.00 |
| 313_H | 317_G | 1.854 | 1.00 |
| 175_L | 178_S | 1.851 | 1.00 |
| 274_S | 297_K | 1.819 | 1.00 |
| 304_W | 338_V | 1.815 | 1.00 |
| 432_Y | 437_I | 1.809 | 1.00 |
| 446_T | 452_L | 1.800 | 1.00 |
| 305_N | 334_C | 1.789 | 1.00 |
| 473_D | 477_K | 1.776 | 1.00 |
| 72_I | 76_R | 1.765 | 1.00 |
| 125_V | 239_L | 1.765 | 1.00 |
| 401_G | 405_E | 1.732 | 1.00 |
| 276_S | 282_E | 1.711 | 1.00 |
| 105_E | 127_P | 1.701 | 1.00 |
| 231_I | 343_D | 1.696 | 1.00 |
| 247_T | 250_Q | 1.685 | 0.99 |
| 301_E | 340_G | 1.676 | 0.99 |
| 190_L | 335_V | 1.672 | 0.99 |
| 395_L | 445_E | 1.642 | 0.99 |
| 402_L | 471_L | 1.639 | 0.99 |
| 118_V | 259_R | 1.628 | 0.99 |
| 263_W | 301_E | 1.617 | 0.99 |
| 96_H | 133_H | 1.615 | 0.99 |
| 116_T | 120_V | 1.609 | 0.99 |
| 325_R | 330_N | 1.592 | 0.99 |
| 269_S | 352_D | 1.590 | 0.99 |
| 315_Y | 323_H | 1.586 | 0.99 |
| 308_D | 312_L | 1.585 | 0.99 |
| 286_G | 304_W | 1.582 | 0.99 |
| 383_V | 416_G | 1.577 | 0.99 |
| 467_H | 470_K | 1.577 | 0.99 |
| 149_S | 168_V | 1.560 | 0.99 |
| 244_P | 329_K | 1.554 | 0.99 |
| 269_S | 272_N | 1.552 | 0.99 |
| 358_E | 368_H | 1.549 | 0.99 |
| 315_Y | 322_L | 1.548 | 0.99 |
| 402_L | 468_I | 1.538 | 0.99 |
| 110_L | 346_M | 1.537 | 0.99 |
| 260_L | 270_P | 1.532 | 0.99 |
| 126_F | 202_K | 1.522 | 0.99 |
| 105_E | 115_W | 1.520 | 0.99 |
| 315_Y | 332_V | 1.515 | 0.99 |
| 248_S | 305_N | 1.509 | 0.99 |
| 72_I | 434_E | 1.506 | 0.99 |
| 214_C | 339_N | 1.505 | 0.99 |
| 214_C | 236_E | 1.500 | 0.99 |
| 283_G | 286_G | 1.498 | 0.99 |
| 111_A | 211_I | 1.477 | 0.98 |
| 82_S | 96_H | 1.475 | 0.98 |
| 446_T | 449_E | 1.471 | 0.98 |
| 455_L | 471_L | 1.468 | 0.98 |
| 383_V | 475_L | 1.466 | 0.98 |
| 424_S | 427_Q | 1.456 | 0.98 |
| 405_E | 472_K | 1.448 | 0.98 |
| 240_V | 338_V | 1.426 | 0.98 |
| 257_R | 261_Q | 1.424 | 0.98 |
| 118_V | 340_G | 1.424 | 0.98 |
| 358_E | 366_N | 1.409 | 0.98 |
| 430_S | 461_T | 1.393 | 0.97 |
| 251_W | 254_F | 1.374 | 0.97 |
| 286_G | 338_V | 1.372 | 0.97 |
| 309_H | 313_H | 1.368 | 0.97 |
| 355_Q | 371_V | 1.367 | 0.97 |
| 228_V | 346_M | 1.348 | 0.97 |
| 439_F | 475_L | 1.348 | 0.97 |
| 356_L | 368_H | 1.342 | 0.96 |
| 244_P | 247_T | 1.335 | 0.96 |
| 402_L | 405_E | 1.319 | 0.96 |
| 194_V | 320_S | 1.317 | 0.96 |
| 207_G | 241_W | 1.315 | 0.96 |
| 307_G | 334_C | 1.307 | 0.96 |
| 274_S | 290_Y | 1.293 | 0.95 |
| 185_L | 236_E | 1.284 | 0.95 |
| 118_V | 239_L | 1.283 | 0.95 |
| 272_N | 352_D | 1.283 | 0.95 |
| 266_F | 349_Y | 1.281 | 0.95 |
| 422_Q | 431_K | 1.280 | 0.95 |
| 110_L | 345_G | 1.280 | 0.95 |
| 95_C | 222_K | 1.278 | 0.95 |
| 118_V | 301_E | 1.276 | 0.95 |
| 239_L | 339_N | 1.275 | 0.95 |
| 447_T | 452_L | 1.273 | 0.95 |
| 464_E | 478_Y | 1.269 | 0.95 |
| 237_A | 342_L | 1.268 | 0.95 |
| 240_V | 286_G | 1.258 | 0.94 |
| 106_L | 378_L | 1.254 | 0.94 |
| 263_W | 340_G | 1.248 | 0.94 |
| 75_R | 434_E | 1.246 | 0.94 |
| 260_L | 275_S | 1.237 | 0.94 |
| 384_A | 432_Y | 1.233 | 0.94 |
| 141_G | 318_N | 1.231 | 0.93 |
| 259_R | 263_W | 1.231 | 0.93 |
| 263_W | 345_G | 1.230 | 0.93 |
| 107_R | 343_D | 1.230 | 0.93 |
| 276_S | 290_Y | 1.228 | 0.93 |
| 252_L | 256_L | 1.227 | 0.93 |
| 150_A | 153_L | 1.225 | 0.93 |
| 394_E | 397_Q | 1.224 | 0.93 |
| 464_E | 474_F | 1.213 | 0.93 |
| 99_F | 228_V | 1.212 | 0.93 |
| 259_R | 340_G | 1.208 | 0.93 |
| 120_V | 415_P | 1.207 | 0.93 |
| 398_V | 443_V | 1.203 | 0.92 |
| 111_A | 342_L | 1.195 | 0.92 |
| 323_H | 330_N | 1.193 | 0.92 |
| 283_G | 304_W | 1.192 | 0.92 |
| 126_F | 200_V | 1.192 | 0.92 |
| 132_H | 215_F | 1.188 | 0.92 |
| 381_I | 417_Y | 1.185 | 0.92 |
| 345_G | 349_Y | 1.184 | 0.92 |
| 264_R | 270_P | 1.176 | 0.91 |
| 359_N | 366_N | 1.175 | 0.91 |
| 134_K | 139_L | 1.174 | 0.91 |
| 261_Q | 265_K | 1.171 | 0.91 |
| 104_V | 108_K | 1.168 | 0.91 |
| 153_L | 162_L | 1.167 | 0.91 |
| 252_L | 287_N | 1.159 | 0.90 |
| 272_N | 291_Y | 1.155 | 0.90 |
| 87_S | 134_K | 1.149 | 0.90 |
| 69_L | 351_Y | 1.143 | 0.90 |
| 379_A | 438_L | 1.142 | 0.90 |
| 254_F | 258_H | 1.137 | 0.89 |
| 133_H | 179_G | 1.134 | 0.89 |
| 141_G | 317_G | 1.133 | 0.89 |
| 290_Y | 298_E | 1.129 | 0.89 |
| 405_E | 469_S | 1.129 | 0.89 |
| 249_N | 285_K | 1.124 | 0.89 |
| 268_M | 348_A | 1.123 | 0.89 |
| 125_V | 209_A | 1.112 | 0.88 |
| 136_G | 140_P | 1.109 | 0.88 |
| 441_V | 455_L | 1.098 | 0.87 |
| 350_L | 374_L | 1.098 | 0.87 |
| 197_L | 200_V | 1.090 | 0.87 |
| 78_F | 106_L | 1.090 | 0.87 |
| 259_R | 303_L | 1.087 | 0.86 |
| 250_Q | 254_F | 1.084 | 0.86 |
| 95_C | 231_I | 1.082 | 0.86 |
| 140_P | 145_F | 1.073 | 0.85 |
| 117_S | 121_F | 1.071 | 0.85 |
| 72_I | 372_L | 1.069 | 0.85 |
| 189_A | 210_Q | 1.067 | 0.85 |
| 275_S | 287_N | 1.063 | 0.85 |
| 79_L | 228_V | 1.057 | 0.84 |
| 466_M | 471_L | 1.056 | 0.84 |
| 228_V | 343_D | 1.056 | 0.84 |
| 472_K | 476_I | 1.055 | 0.84 |
| 110_L | 349_Y | 1.055 | 0.84 |
| 123_E | 400_Q | 1.055 | 0.84 |
| 186_L | 190_L | 1.049 | 0.84 |
| 253_D | 257_R | 1.049 | 0.84 |
| 249_N | 305_N | 1.046 | 0.83 |
| 260_L | 264_R | 1.044 | 0.83 |
| 276_S | 279_Q | 1.041 | 0.83 |
| 137_P | 317_G | 1.038 | 0.83 |
| 381_I | 435_M | 1.038 | 0.83 |
| 102_L | 381_I | 1.032 | 0.82 |
| 376_P | 439_F | 1.029 | 0.82 |
| 118_V | 263_W | 1.029 | 0.82 |
| 315_Y | 321_K | 1.028 | 0.82 |
| 397_Q | 401_G | 1.028 | 0.82 |
| 360_S | 366_N | 1.027 | 0.82 |
| 189_A | 208_L | 1.026 | 0.82 |
| 357_T | 369_R | 1.025 | 0.82 |
| 323_H | 332_V | 1.023 | 0.81 |
| 291_Y | 348_A | 1.021 | 0.81 |
| 391_P | 396_R | 1.021 | 0.81 |
| 391_P | 394_E | 1.016 | 0.81 |
| 153_L | 159_D | 1.015 | 0.81 |
| 349_Y | 378_L | 1.012 | 0.80 |
| 104_V | 127_P | 1.011 | 0.80 |
| 185_L | 238_S | 1.011 | 0.80 |
| 164_K | 167_L | 1.006 | 0.80 |
| 343_D | 346_M | 1.004 | 0.80 |
| 466_M | 474_F | 1.000 | 0.79 |
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 | |
| 3iklA | 2 | 0.7505 | 100 | 0.417 | Contact Map |
| 2zt5A | 1 | 0.833 | 100 | 0.498 | Contact Map |
| 1g5hA | 4 | 0.8433 | 100 | 0.506 | Contact Map |
| 1atiA | 2 | 0.8124 | 100 | 0.52 | Contact Map |
| 3ialA | 2 | 0.7856 | 100 | 0.627 | Contact Map |
| 1nj8A | 4 | 0.7691 | 100 | 0.64 | Contact Map |
| 4ncxA | 2 | 0.732 | 100 | 0.64 | Contact Map |
| 1nj1A | 1 | 0.7649 | 100 | 0.644 | Contact Map |
| 3a32A | 1 | 0.7732 | 100 | 0.647 | Contact Map |
| 4hvcA | 2 | 0.7835 | 100 | 0.652 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)