| ybgh |
| ID: | 1421337893 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 493 (476) | ||
| Sequences: | 2258 (1694.1) | ||
| Seq/Len: | 4.744 | ||
| Nf(neff/√len): | 77.6 |
Jackhmmer Results: (2014_04_16)
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: 4.744).
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 |
| 369_S | 373_G | 2.953 | 1.00 |
| 457_E | 460_D | 2.510 | 1.00 |
| 161_A | 173_L | 2.406 | 1.00 |
| 237_V | 240_L | 2.246 | 1.00 |
| 68_L | 73_L | 2.207 | 1.00 |
| 256_R | 259_E | 2.137 | 1.00 |
| 253_K | 256_R | 2.093 | 1.00 |
| 455_Y | 458_V | 2.081 | 1.00 |
| 238_Y | 241_I | 2.061 | 1.00 |
| 235_W | 239_A | 1.938 | 1.00 |
| 223_T | 227_I | 1.917 | 1.00 |
| 239_A | 242_V | 1.869 | 1.00 |
| 455_Y | 460_D | 1.867 | 1.00 |
| 333_K | 336_V | 1.867 | 1.00 |
| 235_W | 240_L | 1.851 | 1.00 |
| 455_Y | 459_F | 1.842 | 1.00 |
| 449_N | 452_I | 1.835 | 1.00 |
| 460_D | 463_T | 1.828 | 1.00 |
| 459_F | 462_I | 1.820 | 1.00 |
| 88_I | 109_I | 1.818 | 1.00 |
| 456_I | 460_D | 1.814 | 1.00 |
| 458_V | 461_Q | 1.807 | 1.00 |
| 237_V | 241_I | 1.805 | 1.00 |
| 44_D | 297_R | 1.780 | 1.00 |
| 73_L | 78_A | 1.776 | 1.00 |
| 460_D | 464_W | 1.760 | 1.00 |
| 459_F | 463_T | 1.743 | 1.00 |
| 241_I | 244_T | 1.733 | 1.00 |
| 301_R | 307_T | 1.724 | 1.00 |
| 162_Q | 311_A | 1.710 | 0.99 |
| 87_A | 179_I | 1.709 | 0.99 |
| 291_I | 295_I | 1.699 | 0.99 |
| 334_E | 337_A | 1.698 | 0.99 |
| 235_W | 238_Y | 1.690 | 0.99 |
| 234_E | 238_Y | 1.689 | 0.99 |
| 458_V | 463_T | 1.679 | 0.99 |
| 245_I | 249_G | 1.656 | 0.99 |
| 21_E | 118_K | 1.654 | 0.99 |
| 376_S | 379_L | 1.646 | 0.99 |
| 18_Q | 22_Y | 1.639 | 0.99 |
| 221_V | 227_I | 1.627 | 0.99 |
| 240_L | 243_A | 1.621 | 0.99 |
| 380_M | 383_G | 1.620 | 0.99 |
| 350_L | 393_F | 1.620 | 0.99 |
| 242_V | 246_I | 1.620 | 0.99 |
| 448_I | 452_I | 1.611 | 0.99 |
| 452_I | 455_Y | 1.609 | 0.99 |
| 240_L | 244_T | 1.599 | 0.99 |
| 229_I | 232_W | 1.598 | 0.99 |
| 369_S | 372_Y | 1.574 | 0.99 |
| 18_Q | 21_E | 1.568 | 0.99 |
| 469_C | 473_V | 1.567 | 0.99 |
| 336_V | 341_T | 1.561 | 0.99 |
| 463_T | 466_A | 1.561 | 0.99 |
| 320_A | 385_A | 1.552 | 0.99 |
| 256_R | 260_N | 1.543 | 0.99 |
| 471_G | 475_M | 1.540 | 0.99 |
| 212_N | 216_L | 1.540 | 0.99 |
| 163_E | 310_T | 1.524 | 0.99 |
| 470_V | 473_V | 1.520 | 0.98 |
| 447_A | 450_Y | 1.517 | 0.98 |
| 323_L | 327_F | 1.517 | 0.98 |
| 294_Y | 297_R | 1.507 | 0.98 |
| 238_Y | 242_V | 1.506 | 0.98 |
| 18_Q | 118_K | 1.505 | 0.98 |
| 38_N | 167_W | 1.500 | 0.98 |
| 234_E | 237_V | 1.498 | 0.98 |
| 455_Y | 462_I | 1.495 | 0.98 |
| 92_V | 109_I | 1.493 | 0.98 |
| 379_L | 383_G | 1.490 | 0.98 |
| 458_V | 462_I | 1.490 | 0.98 |
| 34_L | 292_S | 1.484 | 0.98 |
| 455_Y | 463_T | 1.476 | 0.98 |
| 457_E | 461_Q | 1.470 | 0.98 |
| 449_N | 454_A | 1.469 | 0.98 |
| 457_E | 463_T | 1.468 | 0.98 |
| 212_N | 215_W | 1.457 | 0.98 |
| 473_V | 477_W | 1.447 | 0.98 |
| 262_K | 265_K | 1.446 | 0.98 |
| 447_A | 452_I | 1.439 | 0.98 |
| 456_I | 459_F | 1.439 | 0.98 |
| 290_S | 295_I | 1.436 | 0.98 |
| 61_T | 111_V | 1.436 | 0.98 |
| 309_P | 312_M | 1.434 | 0.98 |
| 455_Y | 464_W | 1.430 | 0.98 |
| 292_S | 295_I | 1.422 | 0.97 |
| 398_A | 418_Y | 1.421 | 0.97 |
| 91_V | 175_A | 1.416 | 0.97 |
| 68_L | 72_V | 1.412 | 0.97 |
| 242_V | 245_I | 1.409 | 0.97 |
| 239_A | 243_A | 1.407 | 0.97 |
| 379_L | 382_L | 1.403 | 0.97 |
| 261_Q | 265_K | 1.398 | 0.97 |
| 459_F | 464_W | 1.380 | 0.97 |
| 468_A | 471_G | 1.378 | 0.97 |
| 458_V | 464_W | 1.373 | 0.97 |
| 232_W | 237_V | 1.365 | 0.96 |
| 252_A | 255_Y | 1.365 | 0.96 |
| 235_W | 241_I | 1.360 | 0.96 |
| 373_G | 377_L | 1.359 | 0.96 |
| 455_Y | 461_Q | 1.356 | 0.96 |
| 451_S | 454_A | 1.354 | 0.96 |
| 456_I | 461_Q | 1.353 | 0.96 |
| 449_N | 455_Y | 1.348 | 0.96 |
| 245_I | 248_L | 1.339 | 0.96 |
| 295_I | 299_V | 1.335 | 0.96 |
| 24_S | 90_H | 1.332 | 0.96 |
| 294_Y | 298_F | 1.327 | 0.96 |
| 361_I | 386_V | 1.326 | 0.96 |
| 232_W | 235_W | 1.324 | 0.96 |
| 293_L | 296_D | 1.321 | 0.96 |
| 447_A | 451_S | 1.316 | 0.95 |
| 277_S | 422_S | 1.313 | 0.95 |
| 82_G | 116_L | 1.313 | 0.95 |
| 373_G | 376_S | 1.287 | 0.95 |
| 22_Y | 118_K | 1.285 | 0.95 |
| 467_L | 470_V | 1.285 | 0.95 |
| 448_I | 451_S | 1.283 | 0.95 |
| 206_T | 210_L | 1.282 | 0.94 |
| 228_T | 232_W | 1.282 | 0.94 |
| 234_E | 241_I | 1.279 | 0.94 |
| 237_V | 242_V | 1.274 | 0.94 |
| 247_G | 250_V | 1.273 | 0.94 |
| 196_R | 199_N | 1.270 | 0.94 |
| 457_E | 464_W | 1.267 | 0.94 |
| 236_S | 239_A | 1.262 | 0.94 |
| 215_W | 218_V | 1.261 | 0.94 |
| 454_A | 459_F | 1.260 | 0.94 |
| 212_N | 217_L | 1.257 | 0.94 |
| 228_T | 231_F | 1.255 | 0.94 |
| 255_Y | 258_A | 1.251 | 0.93 |
| 261_Q | 264_R | 1.249 | 0.93 |
| 467_L | 473_V | 1.247 | 0.93 |
| 450_Y | 455_Y | 1.247 | 0.93 |
| 205_A | 208_F | 1.241 | 0.93 |
| 292_S | 296_D | 1.240 | 0.93 |
| 76_R | 189_N | 1.239 | 0.93 |
| 86_M | 117_F | 1.239 | 0.93 |
| 200_K | 203_L | 1.239 | 0.93 |
| 62_P | 69_A | 1.236 | 0.93 |
| 211_P | 214_G | 1.234 | 0.93 |
| 467_L | 471_G | 1.234 | 0.93 |
| 236_S | 240_L | 1.229 | 0.93 |
| 210_L | 214_G | 1.217 | 0.92 |
| 464_W | 468_A | 1.217 | 0.92 |
| 236_S | 241_I | 1.209 | 0.92 |
| 353_G | 357_A | 1.208 | 0.92 |
| 381_V | 385_A | 1.205 | 0.92 |
| 143_M | 147_G | 1.197 | 0.91 |
| 251_L | 255_Y | 1.196 | 0.91 |
| 280_F | 390_A | 1.194 | 0.91 |
| 61_T | 64_L | 1.193 | 0.91 |
| 255_Y | 259_E | 1.192 | 0.91 |
| 192_F | 197_G | 1.192 | 0.91 |
| 456_I | 463_T | 1.185 | 0.91 |
| 451_S | 455_Y | 1.183 | 0.91 |
| 461_Q | 464_W | 1.182 | 0.91 |
| 448_I | 455_Y | 1.178 | 0.90 |
| 475_M | 479_Y | 1.177 | 0.90 |
| 254_I | 258_A | 1.176 | 0.90 |
| 464_W | 467_L | 1.169 | 0.90 |
| 378_P | 382_L | 1.158 | 0.89 |
| 375_S | 379_L | 1.157 | 0.89 |
| 233_K | 236_S | 1.157 | 0.89 |
| 460_D | 466_A | 1.156 | 0.89 |
| 295_I | 298_F | 1.155 | 0.89 |
| 234_E | 240_L | 1.154 | 0.89 |
| 329_A | 333_K | 1.150 | 0.89 |
| 463_T | 469_C | 1.148 | 0.89 |
| 343_R | 346_G | 1.147 | 0.89 |
| 221_V | 226_L | 1.143 | 0.89 |
| 229_I | 233_K | 1.141 | 0.89 |
| 463_T | 467_L | 1.140 | 0.88 |
| 213_W | 216_L | 1.139 | 0.88 |
| 144_Y | 391_E | 1.138 | 0.88 |
| 453_N | 456_I | 1.135 | 0.88 |
| 213_W | 217_L | 1.134 | 0.88 |
| 224_P | 228_T | 1.133 | 0.88 |
| 278_M | 426_A | 1.132 | 0.88 |
| 454_A | 460_D | 1.132 | 0.88 |
| 73_L | 81_L | 1.124 | 0.88 |
| 454_A | 464_W | 1.122 | 0.87 |
| 262_K | 266_E | 1.121 | 0.87 |
| 466_A | 470_V | 1.116 | 0.87 |
| 462_I | 466_A | 1.115 | 0.87 |
| 302_D | 307_T | 1.113 | 0.87 |
| 464_W | 470_V | 1.112 | 0.87 |
| 22_Y | 147_G | 1.110 | 0.87 |
| 232_W | 238_Y | 1.110 | 0.87 |
| 460_D | 467_L | 1.109 | 0.87 |
| 454_A | 458_V | 1.108 | 0.87 |
| 293_L | 297_R | 1.107 | 0.86 |
| 222_A | 227_I | 1.107 | 0.86 |
| 218_V | 221_V | 1.106 | 0.86 |
| 89_G | 113_G | 1.106 | 0.86 |
| 258_A | 261_Q | 1.106 | 0.86 |
| 454_A | 462_I | 1.105 | 0.86 |
| 460_D | 465_G | 1.103 | 0.86 |
| 324_C | 389_F | 1.103 | 0.86 |
| 456_I | 464_W | 1.099 | 0.86 |
| 281_W | 395_D | 1.099 | 0.86 |
| 33_I | 37_T | 1.091 | 0.85 |
| 460_D | 470_V | 1.089 | 0.85 |
| 375_S | 378_P | 1.086 | 0.85 |
| 336_V | 339_N | 1.085 | 0.85 |
| 363_T | 366_A | 1.083 | 0.85 |
| 471_G | 479_Y | 1.076 | 0.84 |
| 395_D | 398_A | 1.074 | 0.84 |
| 233_K | 237_V | 1.067 | 0.84 |
| 295_I | 380_M | 1.066 | 0.84 |
| 66_G | 412_G | 1.066 | 0.84 |
| 455_Y | 466_A | 1.065 | 0.83 |
| 313_F | 377_L | 1.060 | 0.83 |
| 361_I | 382_L | 1.059 | 0.83 |
| 447_A | 453_N | 1.050 | 0.82 |
| 454_A | 457_E | 1.050 | 0.82 |
| 450_Y | 454_A | 1.050 | 0.82 |
| 316_I | 381_V | 1.049 | 0.82 |
| 337_A | 340_R | 1.048 | 0.82 |
| 42_Y | 50_L | 1.047 | 0.82 |
| 152_I | 322_M | 1.043 | 0.82 |
| 252_A | 256_R | 1.041 | 0.81 |
| 330_W | 333_K | 1.040 | 0.81 |
| 140_F | 403_T | 1.040 | 0.81 |
| 148_N | 317_N | 1.039 | 0.81 |
| 412_G | 416_G | 1.036 | 0.81 |
| 228_T | 233_K | 1.036 | 0.81 |
| 457_E | 462_I | 1.035 | 0.81 |
| 220_L | 224_P | 1.035 | 0.81 |
| 145_A | 325_G | 1.034 | 0.81 |
| 333_K | 337_A | 1.031 | 0.81 |
| 458_V | 469_C | 1.028 | 0.80 |
| 378_P | 383_G | 1.026 | 0.80 |
| 201_K | 208_F | 1.023 | 0.80 |
| 450_Y | 457_E | 1.023 | 0.80 |
| 473_V | 476_I | 1.019 | 0.80 |
| 369_S | 374_H | 1.014 | 0.79 |
| 465_G | 470_V | 1.013 | 0.79 |
| 244_T | 249_G | 1.007 | 0.78 |
| 458_V | 465_G | 1.005 | 0.78 |
| 464_W | 473_V | 1.004 | 0.78 |
| 466_A | 469_C | 1.003 | 0.78 |
| 294_Y | 299_V | 1.003 | 0.78 |
| 224_P | 227_I | 1.002 | 0.78 |
| 215_W | 219_L | 1.001 | 0.78 |
| 80_M | 186_L | 1.000 | 0.78 |
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 | |
| 4q65A | 1 | 0.8844 | 100 | 0.685 | Contact Map |
| 2xutA | 3 | 0.8641 | 100 | 0.698 | Contact Map |
| 4oh3A | 2 | 0.9594 | 100 | 0.702 | Contact Map |
| 4tphA | 2 | 0.8884 | 100 | 0.717 | Contact Map |
| 4ikvA | 1 | 0.9432 | 100 | 0.73 | Contact Map |
| 4d2bA | 1 | 0.8702 | 100 | 0.734 | Contact Map |
| 1pw4A | 1 | 0.8276 | 99.9 | 0.82 | Contact Map |
| 4j05A | 2 | 0.7606 | 99.9 | 0.823 | Contact Map |
| 4pypA | 1 | 0.8519 | 99.9 | 0.829 | Contact Map |
| 4m64A | 4 | 0.854 | 99.9 | 0.829 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)