| corc |
| ID: | 1510620516 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 455 (433) | ||
| Sequences: | 5071 (3133.3) | ||
| Seq/Len: | 11.711 | ||
| Nf(neff/√len): | 150.6 |
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: 11.711).
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 |
| 235_L | 334_I | 4.516 | 1.00 |
| 370_I | 437_V | 3.977 | 1.00 |
| 408_K | 413_D | 3.662 | 1.00 |
| 402_I | 435_F | 3.352 | 1.00 |
| 323_V | 334_I | 2.975 | 1.00 |
| 369_R | 425_L | 2.963 | 1.00 |
| 243_T | 246_Q | 2.908 | 1.00 |
| 278_D | 296_R | 2.835 | 1.00 |
| 261_V | 295_L | 2.826 | 1.00 |
| 237_V | 262_V | 2.675 | 1.00 |
| 235_L | 331_T | 2.641 | 1.00 |
| 414_T | 423_K | 2.605 | 1.00 |
| 305_T | 313_K | 2.577 | 1.00 |
| 242_D | 246_Q | 2.552 | 1.00 |
| 301_I | 310_I | 2.549 | 1.00 |
| 139_M | 142_K | 2.543 | 1.00 |
| 369_R | 434_W | 2.439 | 1.00 |
| 238_I | 261_V | 2.423 | 1.00 |
| 323_V | 331_T | 2.409 | 1.00 |
| 22_F | 150_P | 2.390 | 1.00 |
| 38_L | 55_S | 2.385 | 1.00 |
| 379_F | 383_F | 2.356 | 1.00 |
| 364_A | 367_T | 2.345 | 1.00 |
| 225_A | 310_I | 2.260 | 1.00 |
| 350_D | 353_D | 2.229 | 1.00 |
| 237_V | 267_K | 2.226 | 1.00 |
| 152_R | 156_V | 2.225 | 1.00 |
| 163_W | 167_V | 2.163 | 1.00 |
| 122_Y | 168_S | 2.156 | 1.00 |
| 425_L | 436_E | 2.155 | 1.00 |
| 421_N | 440_Q | 2.133 | 1.00 |
| 423_K | 438_S | 2.115 | 1.00 |
| 41_E | 145_A | 2.110 | 1.00 |
| 171_G | 175_M | 2.095 | 1.00 |
| 20_A | 77_G | 2.054 | 1.00 |
| 421_N | 438_S | 2.046 | 1.00 |
| 238_I | 247_A | 2.037 | 1.00 |
| 213_Y | 344_L | 2.015 | 1.00 |
| 54_T | 152_R | 2.010 | 1.00 |
| 426_D | 434_W | 2.001 | 1.00 |
| 273_Y | 298_I | 2.000 | 1.00 |
| 257_S | 275_Y | 1.952 | 1.00 |
| 54_T | 148_T | 1.952 | 1.00 |
| 37_A | 141_L | 1.943 | 1.00 |
| 64_E | 159_Y | 1.927 | 1.00 |
| 414_T | 421_N | 1.916 | 1.00 |
| 20_A | 73_V | 1.911 | 1.00 |
| 416_Q | 421_N | 1.899 | 1.00 |
| 341_Y | 345_F | 1.881 | 1.00 |
| 363_Q | 367_T | 1.878 | 1.00 |
| 379_F | 398_L | 1.878 | 1.00 |
| 398_L | 435_F | 1.875 | 1.00 |
| 290_R | 293_K | 1.870 | 1.00 |
| 42_Q | 56_L | 1.824 | 1.00 |
| 369_R | 436_E | 1.819 | 1.00 |
| 240_I | 264_N | 1.792 | 1.00 |
| 146_V | 150_P | 1.788 | 1.00 |
| 197_S | 214_M | 1.783 | 1.00 |
| 338_K | 342_E | 1.782 | 1.00 |
| 242_D | 247_A | 1.770 | 1.00 |
| 264_N | 292_N | 1.763 | 1.00 |
| 379_F | 437_V | 1.749 | 1.00 |
| 374_M | 398_L | 1.721 | 1.00 |
| 236_V | 250_V | 1.713 | 1.00 |
| 240_I | 292_N | 1.705 | 1.00 |
| 228_I | 335_V | 1.699 | 1.00 |
| 249_R | 253_Q | 1.696 | 1.00 |
| 147_I | 150_P | 1.695 | 1.00 |
| 374_M | 379_F | 1.690 | 1.00 |
| 223_K | 227_D | 1.684 | 1.00 |
| 54_T | 149_T | 1.679 | 1.00 |
| 426_D | 433_N | 1.662 | 1.00 |
| 338_K | 353_D | 1.638 | 1.00 |
| 240_I | 271_L | 1.621 | 1.00 |
| 370_I | 398_L | 1.613 | 1.00 |
| 401_Y | 417_I | 1.597 | 1.00 |
| 26_C | 147_I | 1.595 | 1.00 |
| 312_Q | 315_I | 1.577 | 1.00 |
| 228_I | 307_I | 1.577 | 1.00 |
| 28_F | 31_V | 1.570 | 1.00 |
| 213_Y | 217_A | 1.554 | 1.00 |
| 55_S | 144_M | 1.551 | 1.00 |
| 310_I | 335_V | 1.541 | 1.00 |
| 264_N | 269_K | 1.541 | 1.00 |
| 363_Q | 366_G | 1.533 | 1.00 |
| 321_I | 336_T | 1.524 | 1.00 |
| 367_T | 438_S | 1.522 | 1.00 |
| 11_V | 15_I | 1.521 | 1.00 |
| 402_I | 424_A | 1.487 | 1.00 |
| 268_D | 330_G | 1.480 | 1.00 |
| 370_I | 379_F | 1.470 | 1.00 |
| 376_I | 380_E | 1.467 | 1.00 |
| 367_T | 436_E | 1.465 | 1.00 |
| 23_F | 72_G | 1.462 | 1.00 |
| 307_I | 340_I | 1.455 | 1.00 |
| 22_F | 147_I | 1.449 | 1.00 |
| 366_G | 439_A | 1.447 | 1.00 |
| 395_V | 404_D | 1.445 | 1.00 |
| 73_V | 77_G | 1.443 | 1.00 |
| 234_Q | 431_Y | 1.436 | 1.00 |
| 131_V | 172_V | 1.434 | 1.00 |
| 362_K | 365_D | 1.428 | 1.00 |
| 167_V | 171_G | 1.417 | 1.00 |
| 57_H | 152_R | 1.409 | 1.00 |
| 273_Y | 321_I | 1.393 | 0.99 |
| 232_R | 330_G | 1.385 | 0.99 |
| 428_E | 433_N | 1.383 | 0.99 |
| 217_A | 344_L | 1.381 | 0.99 |
| 303_E | 332_S | 1.381 | 0.99 |
| 68_T | 162_V | 1.373 | 0.99 |
| 150_P | 153_W | 1.370 | 0.99 |
| 25_A | 143_V | 1.367 | 0.99 |
| 228_I | 340_I | 1.364 | 0.99 |
| 39_E | 56_L | 1.364 | 0.99 |
| 321_I | 334_I | 1.359 | 0.99 |
| 403_L | 432_I | 1.355 | 0.99 |
| 265_N | 269_K | 1.343 | 0.99 |
| 233_T | 330_G | 1.341 | 0.99 |
| 236_V | 256_F | 1.341 | 0.99 |
| 342_E | 353_D | 1.340 | 0.99 |
| 239_D | 242_D | 1.327 | 0.99 |
| 268_D | 331_T | 1.325 | 0.99 |
| 305_T | 310_I | 1.322 | 0.99 |
| 232_R | 268_D | 1.321 | 0.99 |
| 142_K | 146_V | 1.312 | 0.99 |
| 402_I | 406_F | 1.310 | 0.99 |
| 278_D | 352_I | 1.303 | 0.99 |
| 55_S | 148_T | 1.298 | 0.99 |
| 262_V | 270_I | 1.289 | 0.99 |
| 58_M | 65_Y | 1.286 | 0.99 |
| 258_R | 350_D | 1.285 | 0.99 |
| 313_K | 317_K | 1.282 | 0.99 |
| 84_G | 120_L | 1.268 | 0.99 |
| 129_E | 133_K | 1.267 | 0.99 |
| 68_T | 154_F | 1.263 | 0.99 |
| 420_F | 437_V | 1.262 | 0.99 |
| 425_L | 434_W | 1.262 | 0.99 |
| 422_F | 435_F | 1.261 | 0.99 |
| 200_A | 204_G | 1.261 | 0.99 |
| 20_A | 24_V | 1.260 | 0.99 |
| 48_P | 52_I | 1.257 | 0.99 |
| 170_A | 174_K | 1.253 | 0.99 |
| 251_Y | 279_L | 1.250 | 0.99 |
| 258_R | 338_K | 1.242 | 0.98 |
| 225_A | 324_V | 1.242 | 0.98 |
| 380_E | 385_T | 1.234 | 0.98 |
| 348_V | 353_D | 1.231 | 0.98 |
| 251_Y | 259_L | 1.229 | 0.98 |
| 298_I | 323_V | 1.222 | 0.98 |
| 257_S | 350_D | 1.217 | 0.98 |
| 423_K | 436_E | 1.215 | 0.98 |
| 338_K | 350_D | 1.208 | 0.98 |
| 237_V | 331_T | 1.202 | 0.98 |
| 399_T | 403_L | 1.201 | 0.98 |
| 77_G | 124_E | 1.201 | 0.98 |
| 271_L | 295_L | 1.171 | 0.98 |
| 27_E | 133_K | 1.168 | 0.97 |
| 257_S | 351_E | 1.167 | 0.97 |
| 149_T | 153_W | 1.167 | 0.97 |
| 78_I | 81_G | 1.165 | 0.97 |
| 26_C | 151_L | 1.157 | 0.97 |
| 23_F | 154_F | 1.154 | 0.97 |
| 156_V | 159_Y | 1.151 | 0.97 |
| 338_K | 348_V | 1.144 | 0.97 |
| 236_V | 254_K | 1.141 | 0.97 |
| 235_L | 267_K | 1.139 | 0.97 |
| 372_G | 398_L | 1.133 | 0.97 |
| 258_R | 351_E | 1.132 | 0.97 |
| 70_Q | 73_V | 1.130 | 0.97 |
| 73_V | 129_E | 1.125 | 0.97 |
| 302_P | 305_T | 1.124 | 0.97 |
| 401_Y | 422_F | 1.121 | 0.97 |
| 399_T | 431_Y | 1.119 | 0.96 |
| 118_F | 122_Y | 1.113 | 0.96 |
| 343_E | 347_T | 1.113 | 0.96 |
| 420_F | 439_A | 1.110 | 0.96 |
| 38_L | 56_L | 1.110 | 0.96 |
| 314_M | 322_V | 1.109 | 0.96 |
| 33_T | 140_P | 1.106 | 0.96 |
| 402_I | 422_F | 1.103 | 0.96 |
| 220_F | 340_I | 1.102 | 0.96 |
| 20_A | 76_A | 1.097 | 0.96 |
| 70_Q | 74_S | 1.097 | 0.96 |
| 234_Q | 373_K | 1.091 | 0.96 |
| 164_L | 167_V | 1.085 | 0.96 |
| 241_N | 264_N | 1.079 | 0.95 |
| 160_P | 164_L | 1.061 | 0.95 |
| 114_V | 118_F | 1.050 | 0.94 |
| 24_V | 28_F | 1.047 | 0.94 |
| 360_I | 374_M | 1.040 | 0.94 |
| 80_L | 120_L | 1.038 | 0.94 |
| 74_S | 121_T | 1.038 | 0.94 |
| 155_H | 159_Y | 1.035 | 0.94 |
| 270_I | 323_V | 1.031 | 0.94 |
| 411_A | 426_D | 1.029 | 0.94 |
| 232_R | 326_D | 1.021 | 0.93 |
| 405_N | 417_I | 1.021 | 0.93 |
| 167_V | 170_A | 1.012 | 0.93 |
| 42_Q | 53_S | 1.011 | 0.93 |
| 49_S | 145_A | 1.011 | 0.93 |
| 349_N | 356_S | 1.007 | 0.93 |
| 260_P | 273_Y | 1.005 | 0.93 |
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 | |
| 4hg0A | 1 | 0.5055 | 100 | 0.534 | Contact Map |
| 3lhhA | 1 | 0.2747 | 100 | 0.766 | Contact Map |
| 3oi8A | 2 | 0.3429 | 99.9 | 0.784 | Contact Map |
| 3ocoA | 2 | 0.2967 | 99.9 | 0.786 | Contact Map |
| 3ocmA | 2 | 0.3275 | 99.9 | 0.79 | Contact Map |
| 3kxrA | 1 | 0.3538 | 99.9 | 0.797 | Contact Map |
| 2v8qE | 1 | 0.5143 | 99.9 | 0.799 | Contact Map |
| 3lv9A | 1 | 0.2857 | 99.9 | 0.799 | Contact Map |
| 4iysA | 1 | 0.3121 | 99.9 | 0.806 | Contact Map |
| 3t4nC | 1 | 0.5253 | 99.9 | 0.817 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)