| yjdlleastfilt |
| ID: | 1397947780 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 0% gaps before running GREMLIN. |
| Length: | 485 (472) | ||
| Sequences: | 5333 (2367.1) | ||
| Seq/Len: | 11.299 | ||
| Nf(neff/√len): | 109.0 |
Jackhmmer Results: (2014_03_19)
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: 11.299).
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 |
| 330_S | 333_S | 2.521 | 1.00 |
| 250_I | 253_M | 2.302 | 1.00 |
| 331_P | 334_R | 2.123 | 1.00 |
| 81_G | 115_L | 2.006 | 1.00 |
| 298_R | 304_E | 1.948 | 1.00 |
| 74_N | 126_E | 1.936 | 1.00 |
| 327_W | 331_P | 1.929 | 1.00 |
| 395_A | 412_Y | 1.876 | 1.00 |
| 67_L | 72_L | 1.871 | 1.00 |
| 160_A | 172_L | 1.871 | 1.00 |
| 20_E | 117_K | 1.826 | 1.00 |
| 358_L | 383_L | 1.781 | 1.00 |
| 239_L | 243_C | 1.779 | 1.00 |
| 250_I | 254_M | 1.773 | 1.00 |
| 329_A | 333_S | 1.771 | 1.00 |
| 327_W | 333_S | 1.748 | 1.00 |
| 327_W | 330_S | 1.744 | 1.00 |
| 23_S | 89_H | 1.742 | 1.00 |
| 306_P | 309_L | 1.701 | 1.00 |
| 310_F | 374_M | 1.698 | 1.00 |
| 17_Q | 20_E | 1.673 | 1.00 |
| 247_A | 250_I | 1.655 | 1.00 |
| 72_L | 77_A | 1.651 | 1.00 |
| 406_G | 410_G | 1.634 | 1.00 |
| 124_L | 127_L | 1.632 | 1.00 |
| 87_L | 108_I | 1.614 | 1.00 |
| 340_R | 343_L | 1.612 | 1.00 |
| 317_A | 382_A | 1.610 | 1.00 |
| 251_A | 254_M | 1.607 | 1.00 |
| 347_F | 390_F | 1.599 | 1.00 |
| 21_Y | 117_K | 1.596 | 1.00 |
| 431_T | 435_Q | 1.589 | 1.00 |
| 86_T | 178_F | 1.573 | 1.00 |
| 330_S | 334_R | 1.570 | 1.00 |
| 17_Q | 117_K | 1.567 | 1.00 |
| 453_E | 457_A | 1.566 | 1.00 |
| 326_A | 330_S | 1.564 | 1.00 |
| 292_I | 296_V | 1.541 | 1.00 |
| 237_Y | 241_I | 1.538 | 1.00 |
| 21_Y | 146_G | 1.534 | 1.00 |
| 238_L | 241_I | 1.528 | 1.00 |
| 291_F | 294_R | 1.526 | 1.00 |
| 124_L | 138_G | 1.513 | 1.00 |
| 366_A | 370_G | 1.509 | 1.00 |
| 88_G | 112_G | 1.507 | 1.00 |
| 58_Y | 117_K | 1.492 | 1.00 |
| 250_I | 255_I | 1.485 | 1.00 |
| 17_Q | 21_Y | 1.485 | 1.00 |
| 288_I | 292_I | 1.484 | 1.00 |
| 397_A | 401_R | 1.460 | 1.00 |
| 143_Y | 147_N | 1.444 | 1.00 |
| 206_K | 209_L | 1.441 | 1.00 |
| 447_F | 451_M | 1.435 | 1.00 |
| 91_V | 108_I | 1.432 | 1.00 |
| 165_G | 168_V | 1.425 | 1.00 |
| 363_A | 366_A | 1.419 | 1.00 |
| 209_L | 213_S | 1.415 | 1.00 |
| 43_D | 294_R | 1.413 | 1.00 |
| 278_W | 392_D | 1.409 | 1.00 |
| 237_Y | 240_A | 1.404 | 0.99 |
| 428_A | 431_T | 1.402 | 0.99 |
| 240_A | 243_C | 1.384 | 0.99 |
| 61_P | 68_A | 1.380 | 0.99 |
| 320_L | 324_V | 1.372 | 0.99 |
| 331_P | 335_G | 1.371 | 0.99 |
| 445_Q | 449_S | 1.368 | 0.99 |
| 235_S | 238_L | 1.367 | 0.99 |
| 404_M | 407_V | 1.365 | 0.99 |
| 277_F | 387_A | 1.356 | 0.99 |
| 326_A | 333_S | 1.343 | 0.99 |
| 450_Q | 454_W | 1.340 | 0.99 |
| 366_A | 369_D | 1.337 | 0.99 |
| 393_P | 397_A | 1.332 | 0.99 |
| 210_P | 213_S | 1.327 | 0.99 |
| 362_D | 366_A | 1.322 | 0.99 |
| 85_M | 116_F | 1.321 | 0.99 |
| 333_S | 338_T | 1.320 | 0.99 |
| 205_V | 209_L | 1.320 | 0.99 |
| 447_F | 450_Q | 1.317 | 0.99 |
| 60_T | 110_I | 1.313 | 0.99 |
| 314_N | 385_G | 1.311 | 0.99 |
| 397_A | 402_L | 1.310 | 0.99 |
| 67_L | 71_L | 1.308 | 0.99 |
| 443_A | 448_F | 1.307 | 0.99 |
| 354_C | 383_L | 1.307 | 0.99 |
| 228_L | 232_N | 1.304 | 0.99 |
| 452_G | 455_T | 1.304 | 0.99 |
| 201_A | 204_S | 1.302 | 0.99 |
| 314_N | 318_V | 1.294 | 0.99 |
| 373_S | 376_V | 1.292 | 0.99 |
| 24_F | 54_A | 1.289 | 0.99 |
| 239_L | 242_V | 1.288 | 0.99 |
| 445_Q | 448_F | 1.285 | 0.99 |
| 212_W | 216_V | 1.277 | 0.99 |
| 450_Q | 453_E | 1.277 | 0.99 |
| 332_E | 335_G | 1.273 | 0.99 |
| 427_V | 431_T | 1.273 | 0.99 |
| 213_S | 217_V | 1.272 | 0.99 |
| 447_F | 452_G | 1.270 | 0.99 |
| 235_S | 239_L | 1.263 | 0.99 |
| 210_P | 215_L | 1.262 | 0.99 |
| 397_A | 400_T | 1.260 | 0.99 |
| 362_D | 365_H | 1.257 | 0.99 |
| 289_S | 292_I | 1.250 | 0.99 |
| 238_L | 242_V | 1.250 | 0.99 |
| 90_V | 174_G | 1.246 | 0.98 |
| 290_L | 294_R | 1.244 | 0.98 |
| 217_V | 220_C | 1.243 | 0.98 |
| 211_V | 214_W | 1.242 | 0.98 |
| 241_I | 244_L | 1.241 | 0.98 |
| 322_G | 326_A | 1.234 | 0.98 |
| 311_Q | 315_A | 1.234 | 0.98 |
| 211_V | 215_L | 1.234 | 0.98 |
| 297_N | 300_A | 1.234 | 0.98 |
| 449_S | 453_E | 1.232 | 0.98 |
| 445_Q | 452_G | 1.232 | 0.98 |
| 91_V | 105_A | 1.231 | 0.98 |
| 287_T | 292_I | 1.231 | 0.98 |
| 72_L | 80_A | 1.224 | 0.98 |
| 448_F | 451_M | 1.220 | 0.98 |
| 236_G | 240_A | 1.216 | 0.98 |
| 253_M | 258_P | 1.216 | 0.98 |
| 88_G | 109_I | 1.215 | 0.98 |
| 286_S | 428_A | 1.215 | 0.98 |
| 75_R | 188_H | 1.215 | 0.98 |
| 333_S | 336_N | 1.215 | 0.98 |
| 255_I | 258_P | 1.215 | 0.98 |
| 449_S | 452_G | 1.214 | 0.98 |
| 192_Q | 195_R | 1.211 | 0.98 |
| 19_W | 22_F | 1.203 | 0.98 |
| 168_V | 171_A | 1.202 | 0.98 |
| 198_D | 201_A | 1.202 | 0.98 |
| 195_R | 198_D | 1.199 | 0.98 |
| 358_L | 379_S | 1.197 | 0.98 |
| 398_Q | 402_L | 1.191 | 0.98 |
| 253_M | 256_K | 1.191 | 0.98 |
| 327_W | 334_R | 1.191 | 0.98 |
| 243_C | 247_A | 1.186 | 0.98 |
| 234_W | 238_L | 1.185 | 0.98 |
| 447_F | 454_W | 1.184 | 0.98 |
| 443_A | 451_M | 1.181 | 0.98 |
| 448_F | 453_E | 1.181 | 0.98 |
| 213_S | 216_V | 1.179 | 0.98 |
| 199_K | 202_L | 1.178 | 0.98 |
| 35_L | 102_L | 1.171 | 0.98 |
| 290_L | 293_D | 1.168 | 0.97 |
| 443_A | 449_S | 1.166 | 0.97 |
| 159_L | 164_Y | 1.165 | 0.97 |
| 19_W | 176_G | 1.165 | 0.97 |
| 446_R | 449_S | 1.162 | 0.97 |
| 281_A | 284_G | 1.162 | 0.97 |
| 121_S | 142_L | 1.161 | 0.97 |
| 42_D | 45_H | 1.161 | 0.97 |
| 394_V | 397_A | 1.155 | 0.97 |
| 32_I | 36_T | 1.150 | 0.97 |
| 207_F | 213_S | 1.150 | 0.97 |
| 243_C | 246_A | 1.147 | 0.97 |
| 33_L | 289_S | 1.146 | 0.97 |
| 324_V | 328_L | 1.146 | 0.97 |
| 420_A | 423_L | 1.144 | 0.97 |
| 405_S | 410_G | 1.144 | 0.97 |
| 116_F | 119_N | 1.140 | 0.97 |
| 254_M | 258_P | 1.133 | 0.97 |
| 326_A | 331_P | 1.131 | 0.97 |
| 378_I | 382_A | 1.130 | 0.97 |
| 113_Y | 117_K | 1.130 | 0.97 |
| 448_F | 454_W | 1.123 | 0.97 |
| 14_V | 145_A | 1.123 | 0.97 |
| 60_T | 63_L | 1.123 | 0.97 |
| 399_I | 402_L | 1.122 | 0.97 |
| 17_Q | 142_L | 1.119 | 0.96 |
| 88_G | 92_L | 1.117 | 0.96 |
| 37_H | 166_W | 1.116 | 0.96 |
| 289_S | 293_D | 1.116 | 0.96 |
| 445_Q | 450_Q | 1.115 | 0.96 |
| 234_W | 240_A | 1.115 | 0.96 |
| 458_C | 462_I | 1.115 | 0.96 |
| 242_V | 246_A | 1.114 | 0.96 |
| 142_L | 146_G | 1.114 | 0.96 |
| 285_G | 289_S | 1.108 | 0.96 |
| 299_Q | 304_E | 1.102 | 0.96 |
| 303_I | 309_L | 1.099 | 0.96 |
| 236_G | 239_L | 1.098 | 0.96 |
| 291_F | 296_V | 1.098 | 0.96 |
| 205_V | 210_P | 1.098 | 0.96 |
| 235_S | 240_A | 1.097 | 0.96 |
| 405_S | 408_L | 1.096 | 0.96 |
| 422_W | 426_V | 1.094 | 0.96 |
| 258_P | 262_R | 1.093 | 0.96 |
| 351_L | 386_F | 1.091 | 0.96 |
| 206_K | 210_P | 1.090 | 0.96 |
| 292_I | 295_F | 1.088 | 0.96 |
| 426_V | 430_Q | 1.088 | 0.96 |
| 329_A | 332_E | 1.087 | 0.96 |
| 87_L | 91_V | 1.087 | 0.96 |
| 92_L | 105_A | 1.085 | 0.96 |
| 250_I | 256_K | 1.084 | 0.96 |
| 64_G | 119_N | 1.084 | 0.96 |
| 295_F | 298_R | 1.083 | 0.96 |
| 166_W | 169_G | 1.081 | 0.95 |
| 284_G | 384_M | 1.076 | 0.95 |
| 291_F | 295_F | 1.075 | 0.95 |
| 337_S | 340_R | 1.073 | 0.95 |
| 161_A | 308_A | 1.071 | 0.95 |
| 424_A | 427_V | 1.071 | 0.95 |
| 113_Y | 116_F | 1.070 | 0.95 |
| 105_A | 109_I | 1.068 | 0.95 |
| 293_D | 296_V | 1.067 | 0.95 |
| 251_A | 255_I | 1.066 | 0.95 |
| 17_Q | 116_F | 1.063 | 0.95 |
| 247_A | 251_A | 1.060 | 0.95 |
| 258_P | 261_R | 1.060 | 0.95 |
| 296_V | 299_Q | 1.057 | 0.95 |
| 444_Y | 449_S | 1.057 | 0.95 |
| 252_R | 255_I | 1.055 | 0.95 |
| 224_V | 227_T | 1.055 | 0.95 |
| 424_A | 428_A | 1.051 | 0.94 |
| 371_Q | 374_M | 1.051 | 0.94 |
| 447_F | 453_E | 1.050 | 0.94 |
| 448_F | 452_G | 1.050 | 0.94 |
| 41_F | 49_L | 1.050 | 0.94 |
| 321_A | 386_F | 1.050 | 0.94 |
| 85_M | 113_Y | 1.049 | 0.94 |
| 329_A | 334_R | 1.049 | 0.94 |
| 93_G | 174_G | 1.049 | 0.94 |
| 30_L | 169_G | 1.048 | 0.94 |
| 237_Y | 242_V | 1.047 | 0.94 |
| 232_N | 239_L | 1.046 | 0.94 |
| 426_V | 429_Q | 1.044 | 0.94 |
| 254_M | 257_F | 1.044 | 0.94 |
| 78_V | 184_F | 1.043 | 0.94 |
| 444_Y | 447_F | 1.042 | 0.94 |
| 250_I | 258_P | 1.037 | 0.94 |
| 234_W | 237_Y | 1.037 | 0.94 |
| 392_D | 396_I | 1.037 | 0.94 |
| 241_I | 245_I | 1.036 | 0.94 |
| 425_G | 428_A | 1.036 | 0.94 |
| 207_F | 210_P | 1.036 | 0.94 |
| 200_K | 203_T | 1.036 | 0.94 |
| 443_A | 446_R | 1.035 | 0.94 |
| 82_A | 177_M | 1.034 | 0.94 |
| 209_L | 212_W | 1.034 | 0.94 |
| 329_A | 336_N | 1.034 | 0.94 |
| 209_L | 214_W | 1.031 | 0.94 |
| 248_Q | 251_A | 1.031 | 0.94 |
| 451_M | 455_T | 1.030 | 0.94 |
| 330_S | 335_G | 1.030 | 0.94 |
| 117_K | 121_S | 1.029 | 0.94 |
| 394_V | 399_I | 1.029 | 0.94 |
| 34_Y | 102_L | 1.028 | 0.94 |
| 246_A | 249_I | 1.027 | 0.94 |
| 206_K | 213_S | 1.024 | 0.93 |
| 444_Y | 448_F | 1.022 | 0.93 |
| 425_G | 429_Q | 1.022 | 0.93 |
| 456_L | 460_A | 1.018 | 0.93 |
| 48_S | 52_A | 1.017 | 0.93 |
| 204_S | 210_P | 1.015 | 0.93 |
| 247_A | 254_M | 1.011 | 0.93 |
| 334_R | 337_S | 1.011 | 0.93 |
| 214_W | 219_L | 1.011 | 0.93 |
| 318_V | 388_E | 1.011 | 0.93 |
| 356_F | 359_L | 1.009 | 0.93 |
| 214_W | 217_V | 1.008 | 0.93 |
| 201_A | 205_V | 1.006 | 0.93 |
| 452_G | 458_C | 1.004 | 0.93 |
| 210_P | 214_W | 1.002 | 0.92 |
| 443_A | 447_F | 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 | |
| 2xutA | 3 | 0.8619 | 100 | 0.629 | Contact Map |
| 4lepA | 2 | 0.9134 | 100 | 0.632 | Contact Map |
| 4apsA | 2 | 0.8866 | 100 | 0.643 | Contact Map |
| 4ikvA | 1 | 0.9464 | 100 | 0.648 | Contact Map |
| 4oh3A | 2 | 0.9526 | 100 | 0.654 | Contact Map |
| 1pw4A | 1 | 0.8371 | 100 | 0.742 | Contact Map |
| 4j05A | 2 | 0.7835 | 100 | 0.75 | Contact Map |
| 3wdoA | 1 | 0.8206 | 99.9 | 0.761 | Contact Map |
| 4ldsA | 2 | 0.8577 | 99.9 | 0.764 | Contact Map |
| 4m64A | 4 | 0.8536 | 99.9 | 0.764 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)