| CyAT |
| ID: | 1497473064 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 480 (477) | ||
| Sequences: | 15150 (12460.4) | ||
| Seq/Len: | 31.761 | ||
| Nf(neff/√len): | 570.5 |
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: 31.761).
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 |
| 255_T | 272_I | 4.653 | 1.00 |
| 274_T | 462_Q | 3.173 | 1.00 |
| 178_R | 204_V | 3.077 | 1.00 |
| 438_L | 454_Y | 2.853 | 1.00 |
| 176_G | 254_D | 2.833 | 1.00 |
| 158_D | 198_K | 2.831 | 1.00 |
| 221_N | 260_Y | 2.710 | 1.00 |
| 296_R | 321_T | 2.679 | 1.00 |
| 167_F | 171_R | 2.666 | 1.00 |
| 162_N | 198_K | 2.651 | 1.00 |
| 177_D | 225_K | 2.599 | 1.00 |
| 410_I | 435_Y | 2.528 | 1.00 |
| 395_D | 413_P | 2.526 | 1.00 |
| 176_G | 462_Q | 2.526 | 1.00 |
| 217_Y | 267_R | 2.507 | 1.00 |
| 206_I | 215_Q | 2.504 | 1.00 |
| 180_G | 224_C | 2.433 | 1.00 |
| 467_D | 470_K | 2.423 | 1.00 |
| 135_Q | 139_T | 2.373 | 1.00 |
| 126_A | 134_D | 2.283 | 1.00 |
| 68_W | 84_F | 2.278 | 1.00 |
| 173_I | 201_A | 2.274 | 1.00 |
| 274_T | 277_A | 2.261 | 1.00 |
| 155_S | 159_Q | 2.225 | 1.00 |
| 146_V | 321_T | 2.195 | 1.00 |
| 336_R | 340_R | 2.189 | 1.00 |
| 135_Q | 138_R | 2.155 | 1.00 |
| 133_I | 158_D | 2.137 | 1.00 |
| 139_T | 142_Q | 2.077 | 1.00 |
| 434_T | 456_G | 2.053 | 1.00 |
| 127_T | 130_Q | 2.046 | 1.00 |
| 178_R | 258_V | 2.040 | 1.00 |
| 175_R | 254_D | 2.035 | 1.00 |
| 164_V | 191_I | 2.035 | 1.00 |
| 173_I | 177_D | 2.000 | 1.00 |
| 435_Y | 455_I | 1.997 | 1.00 |
| 178_R | 202_A | 1.992 | 1.00 |
| 326_R | 329_R | 1.982 | 1.00 |
| 158_D | 245_D | 1.971 | 1.00 |
| 189_T | 303_M | 1.970 | 1.00 |
| 287_R | 431_A | 1.942 | 1.00 |
| 277_A | 406_S | 1.941 | 1.00 |
| 143_V | 151_W | 1.939 | 1.00 |
| 161_S | 198_K | 1.939 | 1.00 |
| 251_E | 254_D | 1.924 | 1.00 |
| 146_V | 341_R | 1.896 | 1.00 |
| 77_A | 81_E | 1.891 | 1.00 |
| 147_F | 187_V | 1.869 | 1.00 |
| 162_N | 166_R | 1.846 | 1.00 |
| 70_Y | 80_M | 1.842 | 1.00 |
| 351_A | 377_D | 1.840 | 1.00 |
| 329_R | 333_E | 1.837 | 1.00 |
| 286_N | 318_A | 1.836 | 1.00 |
| 174_G | 177_D | 1.836 | 1.00 |
| 212_Y | 216_T | 1.835 | 1.00 |
| 337_T | 341_R | 1.811 | 1.00 |
| 141_D | 155_S | 1.807 | 1.00 |
| 164_V | 195_A | 1.789 | 1.00 |
| 439_N | 443_K | 1.773 | 1.00 |
| 255_T | 462_Q | 1.764 | 1.00 |
| 258_V | 465_L | 1.763 | 1.00 |
| 412_W | 425_P | 1.758 | 1.00 |
| 253_E | 274_T | 1.755 | 1.00 |
| 295_D | 344_T | 1.732 | 1.00 |
| 280_N | 432_N | 1.727 | 1.00 |
| 152_L | 187_V | 1.724 | 1.00 |
| 219_L | 224_C | 1.723 | 1.00 |
| 221_N | 267_R | 1.721 | 1.00 |
| 323_V | 343_I | 1.707 | 1.00 |
| 160_R | 188_E | 1.699 | 1.00 |
| 76_D | 79_V | 1.682 | 1.00 |
| 102_P | 106_S | 1.675 | 1.00 |
| 435_Y | 453_L | 1.671 | 1.00 |
| 296_R | 323_V | 1.670 | 1.00 |
| 147_F | 150_E | 1.668 | 1.00 |
| 192_N | 228_L | 1.659 | 1.00 |
| 158_D | 162_N | 1.657 | 1.00 |
| 57_V | 66_V | 1.651 | 1.00 |
| 330_D | 333_E | 1.641 | 1.00 |
| 82_S | 86_Q | 1.635 | 1.00 |
| 134_D | 138_R | 1.635 | 1.00 |
| 216_T | 220_E | 1.609 | 1.00 |
| 97_Q | 100_I | 1.596 | 1.00 |
| 133_I | 198_K | 1.584 | 1.00 |
| 126_A | 130_Q | 1.578 | 1.00 |
| 146_V | 151_W | 1.572 | 1.00 |
| 253_E | 276_Q | 1.565 | 1.00 |
| 88_V | 92_D | 1.560 | 1.00 |
| 468_D | 472_K | 1.555 | 1.00 |
| 442_Q | 454_Y | 1.541 | 1.00 |
| 153_T | 156_E | 1.530 | 1.00 |
| 295_D | 370_R | 1.516 | 1.00 |
| 461_A | 475_F | 1.505 | 1.00 |
| 68_W | 80_M | 1.505 | 1.00 |
| 177_D | 201_A | 1.499 | 1.00 |
| 181_V | 192_N | 1.496 | 1.00 |
| 230_S | 233_Y | 1.495 | 1.00 |
| 399_L | 408_W | 1.489 | 1.00 |
| 152_L | 191_I | 1.484 | 1.00 |
| 143_V | 321_T | 1.482 | 1.00 |
| 371_L | 397_I | 1.471 | 1.00 |
| 188_E | 230_S | 1.468 | 1.00 |
| 434_T | 478_H | 1.465 | 1.00 |
| 75_F | 80_M | 1.463 | 1.00 |
| 470_K | 474_A | 1.453 | 1.00 |
| 436_Y | 478_H | 1.452 | 1.00 |
| 306_D | 402_A | 1.451 | 1.00 |
| 204_V | 222_S | 1.445 | 1.00 |
| 132_F | 194_M | 1.439 | 1.00 |
| 221_N | 467_D | 1.438 | 1.00 |
| 143_V | 146_V | 1.435 | 1.00 |
| 296_R | 343_I | 1.431 | 1.00 |
| 217_Y | 260_Y | 1.422 | 1.00 |
| 55_N | 68_W | 1.412 | 1.00 |
| 373_L | 399_L | 1.412 | 1.00 |
| 210_H | 218_I | 1.410 | 1.00 |
| 132_F | 136_A | 1.400 | 0.99 |
| 272_I | 465_L | 1.388 | 0.99 |
| 446_P | 449_V | 1.388 | 0.99 |
| 277_A | 460_L | 1.386 | 0.99 |
| 347_N | 408_W | 1.385 | 0.99 |
| 148_E | 326_R | 1.381 | 0.99 |
| 210_H | 304_C | 1.378 | 0.99 |
| 195_A | 199_A | 1.371 | 0.99 |
| 301_S | 307_L | 1.370 | 0.99 |
| 273_I | 461_A | 1.370 | 0.99 |
| 131_L | 279_S | 1.367 | 0.99 |
| 409_S | 455_I | 1.367 | 0.99 |
| 129_H | 275_H | 1.365 | 0.99 |
| 150_E | 187_V | 1.365 | 0.99 |
| 323_V | 337_T | 1.364 | 0.99 |
| 116_Y | 447_V | 1.345 | 0.99 |
| 354_D | 383_L | 1.344 | 0.99 |
| 250_A | 254_D | 1.339 | 0.99 |
| 89_E | 93_Q | 1.331 | 0.99 |
| 190_I | 312_I | 1.327 | 0.99 |
| 158_D | 161_S | 1.327 | 0.99 |
| 173_I | 179_V | 1.326 | 0.99 |
| 307_L | 347_N | 1.326 | 0.99 |
| 325_I | 337_T | 1.322 | 0.99 |
| 381_L | 385_A | 1.320 | 0.99 |
| 167_F | 170_S | 1.318 | 0.99 |
| 282_I | 317_S | 1.317 | 0.99 |
| 202_A | 255_T | 1.315 | 0.99 |
| 197_L | 256_A | 1.310 | 0.99 |
| 212_Y | 237_E | 1.303 | 0.99 |
| 315_T | 320_A | 1.302 | 0.99 |
| 132_F | 158_D | 1.301 | 0.99 |
| 183_A | 192_N | 1.299 | 0.99 |
| 145_V | 190_I | 1.297 | 0.99 |
| 220_E | 267_R | 1.289 | 0.99 |
| 405_A | 455_I | 1.282 | 0.99 |
| 292_N | 295_D | 1.276 | 0.99 |
| 24_T | 27_L | 1.276 | 0.99 |
| 128_L | 278_A | 1.275 | 0.99 |
| 276_Q | 458_A | 1.269 | 0.99 |
| 380_P | 383_L | 1.268 | 0.99 |
| 184_K | 230_S | 1.267 | 0.99 |
| 310_Y | 408_W | 1.263 | 0.99 |
| 430_L | 433_Q | 1.259 | 0.99 |
| 145_V | 187_V | 1.258 | 0.99 |
| 129_H | 250_A | 1.258 | 0.99 |
| 131_L | 283_Q | 1.258 | 0.99 |
| 136_A | 158_D | 1.254 | 0.99 |
| 203_Y | 309_V | 1.252 | 0.99 |
| 454_Y | 476_I | 1.251 | 0.99 |
| 405_A | 409_S | 1.246 | 0.98 |
| 295_D | 320_A | 1.235 | 0.98 |
| 111_A | 115_Q | 1.220 | 0.98 |
| 439_N | 445_C | 1.215 | 0.98 |
| 182_L | 215_Q | 1.214 | 0.98 |
| 103_L | 107_Q | 1.205 | 0.98 |
| 281_T | 408_W | 1.204 | 0.98 |
| 371_L | 395_D | 1.199 | 0.98 |
| 70_Y | 75_F | 1.199 | 0.98 |
| 271_V | 461_A | 1.198 | 0.98 |
| 315_T | 322_L | 1.191 | 0.98 |
| 342_G | 368_S | 1.187 | 0.98 |
| 229_D | 233_Y | 1.182 | 0.98 |
| 298_I | 325_I | 1.181 | 0.98 |
| 223_S | 466_N | 1.180 | 0.98 |
| 81_E | 85_T | 1.179 | 0.98 |
| 222_S | 260_Y | 1.177 | 0.98 |
| 397_I | 413_P | 1.176 | 0.98 |
| 347_N | 375_S | 1.175 | 0.98 |
| 375_S | 408_W | 1.175 | 0.98 |
| 109_D | 112_L | 1.173 | 0.98 |
| 93_Q | 104_R | 1.169 | 0.97 |
| 310_Y | 347_N | 1.167 | 0.97 |
| 299_G | 324_M | 1.162 | 0.97 |
| 333_E | 336_R | 1.150 | 0.97 |
| 436_Y | 480_E | 1.149 | 0.97 |
| 213_E | 217_Y | 1.141 | 0.97 |
| 86_Q | 109_D | 1.138 | 0.97 |
| 345_I | 371_L | 1.137 | 0.97 |
| 273_I | 406_S | 1.137 | 0.97 |
| 374_L | 379_I | 1.136 | 0.97 |
| 3_F | 7_Y | 1.130 | 0.97 |
| 347_N | 399_L | 1.125 | 0.97 |
| 12_Q | 15_P | 1.125 | 0.97 |
| 166_R | 246_L | 1.121 | 0.97 |
| 257_Y | 273_I | 1.117 | 0.96 |
| 102_P | 107_Q | 1.116 | 0.96 |
| 79_V | 82_S | 1.116 | 0.96 |
| 300_I | 349_V | 1.115 | 0.96 |
| 307_L | 375_S | 1.113 | 0.96 |
| 210_H | 215_Q | 1.110 | 0.96 |
| 311_D | 347_N | 1.105 | 0.96 |
| 104_R | 107_Q | 1.103 | 0.96 |
| 180_G | 222_S | 1.102 | 0.96 |
| 150_E | 160_R | 1.102 | 0.96 |
| 281_T | 407_I | 1.102 | 0.96 |
| 103_L | 106_S | 1.102 | 0.96 |
| 49_P | 52_Y | 1.096 | 0.96 |
| 259_I | 403_T | 1.096 | 0.96 |
| 66_V | 84_F | 1.095 | 0.96 |
| 129_H | 197_L | 1.091 | 0.96 |
| 297_I | 315_T | 1.090 | 0.96 |
| 180_G | 206_I | 1.088 | 0.96 |
| 282_I | 314_G | 1.086 | 0.96 |
| 379_I | 396_V | 1.077 | 0.95 |
| 160_R | 191_I | 1.077 | 0.95 |
| 171_R | 226_I | 1.075 | 0.95 |
| 164_V | 228_L | 1.075 | 0.95 |
| 23_F | 57_V | 1.072 | 0.95 |
| 133_I | 162_N | 1.070 | 0.95 |
| 192_N | 196_V | 1.068 | 0.95 |
| 17_A | 20_P | 1.067 | 0.95 |
| 180_G | 219_L | 1.058 | 0.95 |
| 181_V | 193_L | 1.052 | 0.95 |
| 71_V | 74_L | 1.051 | 0.94 |
| 433_Q | 459_G | 1.048 | 0.94 |
| 130_Q | 133_I | 1.035 | 0.94 |
| 213_E | 267_R | 1.034 | 0.94 |
| 133_I | 161_S | 1.031 | 0.94 |
| 436_Y | 456_G | 1.030 | 0.94 |
| 157_L | 191_I | 1.028 | 0.94 |
| 213_E | 216_T | 1.027 | 0.94 |
| 209_D | 327_D | 1.024 | 0.93 |
| 260_Y | 270_G | 1.024 | 0.93 |
| 354_D | 380_P | 1.024 | 0.93 |
| 295_D | 345_I | 1.023 | 0.93 |
| 379_I | 398_S | 1.022 | 0.93 |
| 143_V | 153_T | 1.022 | 0.93 |
| 298_I | 337_T | 1.021 | 0.93 |
| 111_A | 114_D | 1.015 | 0.93 |
| 104_R | 110_Y | 1.014 | 0.93 |
| 284_D | 431_A | 1.014 | 0.93 |
| 160_R | 163_Q | 1.013 | 0.93 |
| 307_L | 408_W | 1.012 | 0.93 |
| 176_G | 255_T | 1.011 | 0.93 |
| 469_Q | 473_D | 1.011 | 0.93 |
| 285_I | 310_Y | 1.009 | 0.93 |
| 184_K | 232_L | 1.000 | 0.92 |
| 146_V | 323_V | 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 | |
| 2vsqA | 1 | 0.975 | 100 | 0.142 | Contact Map |
| 4dg8A | 1 | 0.7521 | 100 | 0.277 | Contact Map |
| 3tsyA | 1 | 0.7688 | 100 | 0.325 | Contact Map |
| 4gr5A | 4 | 0.8812 | 100 | 0.326 | Contact Map |
| 1amuA | 2 | 0.75 | 100 | 0.335 | Contact Map |
| 4iz6A | 2 | 0.7708 | 100 | 0.339 | Contact Map |
| 3wvnA | 2 | 0.7188 | 100 | 0.35 | Contact Map |
| 4d4iA | 1 | 0 | 100 | 0.352 | Contact Map |
| 3wv4A | 2 | 0.7292 | 100 | 0.356 | Contact Map |
| 3vnrA | 1 | 0.7333 | 100 | 0.358 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)