| cyc tgac |
| ID: | 1509127131 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 475 (447) | ||
| Sequences: | 18216 (15372.7) | ||
| Seq/Len: | 40.752 | ||
| Nf(neff/√len): | 727.1 |
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: 40.752).
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 |
| 85_I | 95_L | 3.471 | 1.00 |
| 289_R | 320_E | 3.444 | 1.00 |
| 327_A | 335_R | 3.125 | 1.00 |
| 219_R | 339_Q | 3.033 | 1.00 |
| 278_A | 321_I | 2.760 | 1.00 |
| 284_F | 440_A | 2.586 | 1.00 |
| 57_E | 151_V | 2.532 | 1.00 |
| 262_A | 272_V | 2.532 | 1.00 |
| 265_R | 330_E | 2.481 | 1.00 |
| 329_F | 448_L | 2.415 | 1.00 |
| 158_V | 163_A | 2.379 | 1.00 |
| 233_V | 430_P | 2.373 | 1.00 |
| 422_W | 438_F | 2.350 | 1.00 |
| 69_E | 73_D | 2.341 | 1.00 |
| 280_V | 444_L | 2.335 | 1.00 |
| 78_R | 174_E | 2.281 | 1.00 |
| 212_D | 346_H | 2.279 | 1.00 |
| 431_D | 435_D | 2.267 | 1.00 |
| 59_D | 151_V | 2.263 | 1.00 |
| 73_D | 77_A | 2.223 | 1.00 |
| 275_A | 332_R | 2.184 | 1.00 |
| 85_I | 137_W | 2.171 | 1.00 |
| 328_S | 331_A | 2.170 | 1.00 |
| 254_D | 446_A | 2.166 | 1.00 |
| 289_R | 322_D | 2.131 | 1.00 |
| 246_L | 435_D | 2.112 | 1.00 |
| 72_I | 142_I | 2.065 | 1.00 |
| 75_L | 178_L | 2.037 | 1.00 |
| 75_L | 175_V | 1.996 | 1.00 |
| 442_A | 446_A | 1.992 | 1.00 |
| 79_H | 174_E | 1.987 | 1.00 |
| 74_R | 178_L | 1.980 | 1.00 |
| 68_L | 175_V | 1.966 | 1.00 |
| 291_T | 318_L | 1.965 | 1.00 |
| 74_R | 77_A | 1.941 | 1.00 |
| 74_R | 182_P | 1.919 | 1.00 |
| 133_P | 136_R | 1.919 | 1.00 |
| 271_G | 337_Q | 1.911 | 1.00 |
| 424_F | 434_I | 1.892 | 1.00 |
| 248_A | 420_T | 1.884 | 1.00 |
| 106_L | 143_C | 1.882 | 1.00 |
| 251_A | 254_D | 1.870 | 1.00 |
| 64_D | 67_R | 1.868 | 1.00 |
| 213_L | 357_E | 1.862 | 1.00 |
| 422_W | 434_I | 1.853 | 1.00 |
| 213_L | 349_V | 1.830 | 1.00 |
| 119_R | 122_A | 1.819 | 1.00 |
| 244_R | 431_D | 1.813 | 1.00 |
| 173_Q | 308_Q | 1.808 | 1.00 |
| 277_F | 370_V | 1.772 | 1.00 |
| 244_R | 426_E | 1.765 | 1.00 |
| 171_L | 310_V | 1.760 | 1.00 |
| 260_A | 264_A | 1.751 | 1.00 |
| 276_A | 445_L | 1.744 | 1.00 |
| 430_P | 433_V | 1.734 | 1.00 |
| 275_A | 336_Y | 1.697 | 1.00 |
| 81_M | 84_A | 1.664 | 1.00 |
| 217_R | 357_E | 1.655 | 1.00 |
| 258_L | 269_P | 1.654 | 1.00 |
| 214_A | 218_A | 1.649 | 1.00 |
| 265_R | 334_R | 1.647 | 1.00 |
| 80_D | 192_T | 1.641 | 1.00 |
| 215_Y | 343_D | 1.638 | 1.00 |
| 282_G | 323_P | 1.636 | 1.00 |
| 301_P | 305_D | 1.627 | 1.00 |
| 212_D | 348_L | 1.612 | 1.00 |
| 411_A | 420_T | 1.604 | 1.00 |
| 127_M | 143_C | 1.600 | 1.00 |
| 338_R | 342_D | 1.587 | 1.00 |
| 213_L | 217_R | 1.586 | 1.00 |
| 279_E | 444_L | 1.580 | 1.00 |
| 353_D | 356_R | 1.578 | 1.00 |
| 87_R | 93_Q | 1.578 | 1.00 |
| 139_L | 162_I | 1.578 | 1.00 |
| 249_D | 419_S | 1.562 | 1.00 |
| 259_K | 413_E | 1.557 | 1.00 |
| 293_N | 368_F | 1.548 | 1.00 |
| 210_E | 214_A | 1.548 | 1.00 |
| 321_I | 336_Y | 1.524 | 1.00 |
| 258_L | 272_V | 1.521 | 1.00 |
| 324_G | 327_A | 1.510 | 1.00 |
| 278_A | 292_L | 1.508 | 1.00 |
| 57_E | 153_R | 1.506 | 1.00 |
| 223_L | 291_T | 1.496 | 1.00 |
| 193_F | 196_Y | 1.493 | 1.00 |
| 279_E | 332_R | 1.490 | 1.00 |
| 219_R | 342_D | 1.487 | 1.00 |
| 261_R | 265_R | 1.484 | 1.00 |
| 232_A | 433_V | 1.483 | 1.00 |
| 218_A | 221_E | 1.478 | 1.00 |
| 280_V | 441_Y | 1.475 | 1.00 |
| 146_R | 152_I | 1.472 | 1.00 |
| 246_L | 438_F | 1.456 | 1.00 |
| 435_D | 439_A | 1.456 | 1.00 |
| 215_Y | 219_R | 1.455 | 1.00 |
| 249_D | 417_R | 1.452 | 1.00 |
| 107_D | 146_R | 1.450 | 1.00 |
| 142_I | 154_L | 1.443 | 1.00 |
| 267_L | 333_A | 1.436 | 1.00 |
| 257_A | 450_A | 1.421 | 1.00 |
| 330_E | 453_E | 1.415 | 1.00 |
| 255_W | 259_K | 1.414 | 1.00 |
| 65_L | 144_A | 1.400 | 0.99 |
| 246_L | 431_D | 1.388 | 0.99 |
| 173_Q | 177_R | 1.387 | 0.99 |
| 123_V | 145_T | 1.386 | 0.99 |
| 349_V | 357_E | 1.363 | 0.99 |
| 63_L | 68_L | 1.360 | 0.99 |
| 214_A | 217_R | 1.357 | 0.99 |
| 64_D | 179_Y | 1.356 | 0.99 |
| 429_F | 434_I | 1.350 | 0.99 |
| 309_I | 313_F | 1.348 | 0.99 |
| 70_R | 182_P | 1.344 | 0.99 |
| 65_L | 105_V | 1.339 | 0.99 |
| 147_L | 153_R | 1.335 | 0.99 |
| 68_L | 154_L | 1.331 | 0.99 |
| 86_V | 162_I | 1.330 | 0.99 |
| 27_P | 91_R | 1.325 | 0.99 |
| 284_F | 437_M | 1.317 | 0.99 |
| 276_A | 448_L | 1.313 | 0.99 |
| 351_C | 355_T | 1.313 | 0.99 |
| 403_P | 406_W | 1.312 | 0.99 |
| 86_V | 161_L | 1.310 | 0.99 |
| 67_R | 182_P | 1.310 | 0.99 |
| 247_T | 421_S | 1.302 | 0.99 |
| 210_E | 213_L | 1.301 | 0.99 |
| 252_D | 256_E | 1.298 | 0.99 |
| 443_G | 447_R | 1.297 | 0.99 |
| 122_A | 126_A | 1.295 | 0.99 |
| 65_L | 69_E | 1.294 | 0.99 |
| 167_S | 310_V | 1.291 | 0.99 |
| 409_H | 422_W | 1.288 | 0.99 |
| 145_T | 155_H | 1.284 | 0.99 |
| 105_V | 146_R | 1.282 | 0.99 |
| 50_V | 53_H | 1.279 | 0.99 |
| 69_E | 105_V | 1.277 | 0.99 |
| 277_F | 409_H | 1.276 | 0.99 |
| 109_A | 149_D | 1.276 | 0.99 |
| 257_A | 446_A | 1.274 | 0.99 |
| 57_E | 60_F | 1.273 | 0.99 |
| 370_V | 373_T | 1.267 | 0.99 |
| 327_A | 331_A | 1.264 | 0.99 |
| 369_P | 373_T | 1.263 | 0.99 |
| 63_L | 152_I | 1.259 | 0.99 |
| 335_R | 339_Q | 1.259 | 0.99 |
| 283_A | 440_A | 1.250 | 0.99 |
| 373_T | 376_L | 1.247 | 0.99 |
| 245_H | 423_D | 1.247 | 0.99 |
| 76_I | 140_F | 1.246 | 0.98 |
| 274_M | 292_L | 1.244 | 0.98 |
| 318_L | 354_V | 1.241 | 0.98 |
| 67_R | 179_Y | 1.239 | 0.98 |
| 127_M | 130_R | 1.239 | 0.98 |
| 248_A | 438_F | 1.238 | 0.98 |
| 261_R | 449_A | 1.235 | 0.98 |
| 67_R | 183_E | 1.234 | 0.98 |
| 354_V | 358_I | 1.234 | 0.98 |
| 270_S | 294_L | 1.228 | 0.98 |
| 331_A | 334_R | 1.218 | 0.98 |
| 436_A | 440_A | 1.216 | 0.98 |
| 69_E | 102_T | 1.215 | 0.98 |
| 269_P | 418_L | 1.213 | 0.98 |
| 340_L | 344_L | 1.207 | 0.98 |
| 127_M | 157_G | 1.202 | 0.98 |
| 37_Y | 312_D | 1.200 | 0.98 |
| 248_A | 442_A | 1.198 | 0.98 |
| 353_D | 357_E | 1.193 | 0.98 |
| 109_A | 146_R | 1.182 | 0.98 |
| 77_A | 97_E | 1.181 | 0.98 |
| 255_W | 418_L | 1.180 | 0.98 |
| 163_A | 168_L | 1.178 | 0.98 |
| 140_F | 156_L | 1.171 | 0.98 |
| 196_Y | 199_W | 1.168 | 0.97 |
| 240_V | 427_G | 1.167 | 0.97 |
| 68_L | 179_Y | 1.153 | 0.97 |
| 78_R | 178_L | 1.144 | 0.97 |
| 71_A | 178_L | 1.138 | 0.97 |
| 273_L | 418_L | 1.133 | 0.97 |
| 254_D | 442_A | 1.128 | 0.97 |
| 73_D | 100_P | 1.125 | 0.97 |
| 215_Y | 346_H | 1.115 | 0.96 |
| 306_I | 309_I | 1.115 | 0.96 |
| 80_D | 83_R | 1.115 | 0.96 |
| 141_E | 157_G | 1.113 | 0.96 |
| 277_F | 441_Y | 1.107 | 0.96 |
| 70_R | 73_D | 1.106 | 0.96 |
| 178_L | 182_P | 1.102 | 0.96 |
| 219_R | 343_D | 1.099 | 0.96 |
| 323_P | 327_A | 1.098 | 0.96 |
| 267_L | 271_G | 1.098 | 0.96 |
| 160_L | 165_G | 1.098 | 0.96 |
| 104_E | 143_C | 1.096 | 0.96 |
| 176_V | 180_A | 1.094 | 0.96 |
| 255_W | 269_P | 1.090 | 0.96 |
| 67_R | 71_A | 1.090 | 0.96 |
| 433_V | 436_A | 1.089 | 0.96 |
| 257_A | 260_A | 1.089 | 0.96 |
| 42_G | 88_P | 1.087 | 0.96 |
| 31_T | 34_Q | 1.086 | 0.96 |
| 256_E | 260_A | 1.086 | 0.96 |
| 166_R | 297_F | 1.084 | 0.96 |
| 351_C | 354_V | 1.081 | 0.95 |
| 280_V | 440_A | 1.079 | 0.95 |
| 349_V | 354_V | 1.074 | 0.95 |
| 85_I | 93_Q | 1.074 | 0.95 |
| 144_A | 152_I | 1.072 | 0.95 |
| 271_G | 341_R | 1.071 | 0.95 |
| 280_V | 284_F | 1.067 | 0.95 |
| 251_A | 446_A | 1.063 | 0.95 |
| 443_G | 446_A | 1.062 | 0.95 |
| 262_A | 267_L | 1.061 | 0.95 |
| 144_A | 154_L | 1.057 | 0.95 |
| 276_A | 441_Y | 1.056 | 0.95 |
| 296_L | 317_I | 1.050 | 0.94 |
| 322_D | 327_A | 1.049 | 0.94 |
| 123_V | 127_M | 1.048 | 0.94 |
| 192_T | 195_D | 1.048 | 0.94 |
| 163_A | 171_L | 1.044 | 0.94 |
| 273_L | 441_Y | 1.041 | 0.94 |
| 242_R | 427_G | 1.041 | 0.94 |
| 274_M | 340_L | 1.039 | 0.94 |
| 84_A | 92_Q | 1.039 | 0.94 |
| 244_R | 424_F | 1.037 | 0.94 |
| 85_I | 138_P | 1.036 | 0.94 |
| 32_A | 200_Q | 1.033 | 0.94 |
| 75_L | 171_L | 1.032 | 0.94 |
| 463_T | 467_Q | 1.029 | 0.94 |
| 439_A | 442_A | 1.029 | 0.94 |
| 240_V | 425_V | 1.025 | 0.93 |
| 112_A | 115_E | 1.024 | 0.93 |
| 366_A | 369_P | 1.023 | 0.93 |
| 254_D | 257_A | 1.022 | 0.93 |
| 252_D | 417_R | 1.021 | 0.93 |
| 121_A | 125_A | 1.015 | 0.93 |
| 446_A | 450_A | 1.013 | 0.93 |
| 323_P | 332_R | 1.012 | 0.93 |
| 245_H | 421_S | 1.012 | 0.93 |
| 370_V | 374_S | 1.009 | 0.93 |
| 70_R | 74_R | 1.009 | 0.93 |
| 377_G | 380_D | 1.005 | 0.93 |
| 222_A | 320_E | 1.003 | 0.93 |
| 148_P | 151_V | 1.003 | 0.93 |
| 61_A | 150_G | 1.002 | 0.92 |
| 322_D | 335_R | 1.002 | 0.92 |
| 69_E | 103_I | 1.001 | 0.92 |
| 248_A | 439_A | 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 | 0.9432 | 100 | 0.137 | Contact Map |
| 1l5aA | 3 | 0.8863 | 100 | 0.138 | Contact Map |
| 4tx3B | 1 | 0.9158 | 100 | 0.154 | Contact Map |
| 2jgpA | 1 | 0.9326 | 100 | 0.164 | Contact Map |
| 4jn3A | 2 | 0.8926 | 100 | 0.181 | Contact Map |
| 4hvmA | 4 | 0.8063 | 100 | 0.184 | Contact Map |
| 4znmA | 2 | 0 | 100 | 0.194 | Contact Map |
| 2xhgA | 1 | 0.9095 | 100 | 0.257 | Contact Map |
| 1q9jA | 2 | 0.7789 | 100 | 0.363 | Contact Map |
| 3fotA | 1 | 0.8842 | 100 | 0.415 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)