| Muscle_without_TAT |
| ID: | 1416336092 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 503 (330) | ||
| Sequences: | 1870 (1296.3) | ||
| Seq/Len: | 5.667 | ||
| Nf(neff/√len): | 71.4 |
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: 5.667).
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 |
| 204_M | 207_D | 3.804 | 1.00 |
| 336_A | 343_V | 3.440 | 1.00 |
| 458_A | 461_T | 3.163 | 1.00 |
| 314_F | 349_T | 2.838 | 1.00 |
| 255_D | 353_P | 2.784 | 1.00 |
| 416_P | 486_I | 2.680 | 1.00 |
| 372_K | 376_Q | 2.629 | 1.00 |
| 198_S | 215_V | 2.624 | 1.00 |
| 202_K | 215_V | 2.618 | 1.00 |
| 317_P | 333_N | 2.516 | 1.00 |
| 261_T | 345_P | 2.508 | 1.00 |
| 200_L | 299_L | 2.489 | 1.00 |
| 201_I | 296_L | 2.487 | 1.00 |
| 476_Y | 480_Y | 2.373 | 1.00 |
| 202_K | 357_D | 2.363 | 1.00 |
| 258_I | 350_T | 2.332 | 1.00 |
| 417_M | 474_P | 2.328 | 1.00 |
| 375_A | 383_I | 2.295 | 1.00 |
| 260_V | 346_A | 2.270 | 1.00 |
| 254_W | 349_T | 2.224 | 1.00 |
| 259_L | 347_V | 2.166 | 1.00 |
| 198_S | 355_A | 2.110 | 1.00 |
| 377_V | 425_V | 1.982 | 1.00 |
| 455_A | 487_K | 1.976 | 1.00 |
| 301_Y | 351_S | 1.957 | 1.00 |
| 198_S | 202_K | 1.953 | 1.00 |
| 474_P | 478_G | 1.917 | 1.00 |
| 280_T | 468_E | 1.896 | 1.00 |
| 212_F | 336_A | 1.884 | 1.00 |
| 212_F | 338_D | 1.876 | 1.00 |
| 259_L | 323_C | 1.872 | 1.00 |
| 204_M | 295_F | 1.865 | 1.00 |
| 326_G | 334_C | 1.843 | 1.00 |
| 407_R | 411_N | 1.840 | 1.00 |
| 198_S | 357_D | 1.815 | 1.00 |
| 217_P | 322_E | 1.798 | 1.00 |
| 261_T | 343_V | 1.746 | 1.00 |
| 464_P | 467_Y | 1.688 | 1.00 |
| 215_V | 256_N | 1.680 | 1.00 |
| 208_L | 292_M | 1.678 | 1.00 |
| 256_N | 356_A | 1.660 | 1.00 |
| 246_T | 249_K | 1.648 | 1.00 |
| 240_R | 243_G | 1.639 | 1.00 |
| 205_A | 213_V | 1.603 | 0.99 |
| 257_A | 319_I | 1.592 | 0.99 |
| 339_F | 343_V | 1.591 | 0.99 |
| 407_R | 410_W | 1.589 | 0.99 |
| 328_I | 334_C | 1.584 | 0.99 |
| 201_I | 215_V | 1.576 | 0.99 |
| 325_M | 334_C | 1.568 | 0.99 |
| 293_V | 305_W | 1.562 | 0.99 |
| 415_G | 421_A | 1.548 | 0.99 |
| 416_P | 483_P | 1.513 | 0.99 |
| 317_P | 328_I | 1.504 | 0.99 |
| 233_L | 399_F | 1.502 | 0.99 |
| 483_P | 487_K | 1.491 | 0.99 |
| 222_W | 237_T | 1.446 | 0.98 |
| 331_T | 341_G | 1.428 | 0.98 |
| 332_S | 383_I | 1.401 | 0.98 |
| 211_T | 263_T | 1.393 | 0.98 |
| 316_V | 345_P | 1.391 | 0.98 |
| 327_E | 367_F | 1.382 | 0.98 |
| 257_A | 349_T | 1.379 | 0.98 |
| 293_V | 348_I | 1.365 | 0.98 |
| 308_P | 312_Y | 1.347 | 0.97 |
| 215_V | 357_D | 1.345 | 0.97 |
| 337_P | 360_V | 1.339 | 0.97 |
| 451_S | 454_V | 1.334 | 0.97 |
| 435_V | 438_F | 1.333 | 0.97 |
| 404_A | 407_R | 1.326 | 0.97 |
| 317_P | 331_T | 1.326 | 0.97 |
| 400_N | 478_G | 1.317 | 0.97 |
| 484_K | 488_T | 1.314 | 0.97 |
| 475_N | 478_G | 1.301 | 0.96 |
| 201_I | 258_I | 1.296 | 0.96 |
| 487_K | 495_F | 1.293 | 0.96 |
| 213_V | 260_V | 1.285 | 0.96 |
| 205_A | 292_M | 1.284 | 0.96 |
| 421_A | 425_V | 1.278 | 0.96 |
| 458_A | 462_L | 1.278 | 0.96 |
| 232_G | 235_G | 1.271 | 0.96 |
| 294_K | 298_Y | 1.269 | 0.96 |
| 455_A | 458_A | 1.266 | 0.96 |
| 262_G | 288_I | 1.266 | 0.96 |
| 223_V | 227_H | 1.265 | 0.96 |
| 204_M | 208_L | 1.260 | 0.96 |
| 390_K | 406_C | 1.243 | 0.95 |
| 372_K | 375_A | 1.241 | 0.95 |
| 403_L | 485_W | 1.239 | 0.95 |
| 201_I | 213_V | 1.233 | 0.95 |
| 440_R | 443_L | 1.225 | 0.95 |
| 454_V | 462_L | 1.221 | 0.94 |
| 477_K | 480_Y | 1.218 | 0.94 |
| 479_V | 483_P | 1.216 | 0.94 |
| 213_V | 258_I | 1.215 | 0.94 |
| 443_L | 446_D | 1.212 | 0.94 |
| 444_S | 447_G | 1.205 | 0.94 |
| 440_R | 446_D | 1.204 | 0.94 |
| 459_E | 462_L | 1.203 | 0.94 |
| 217_P | 256_N | 1.203 | 0.94 |
| 463_Y | 466_N | 1.198 | 0.94 |
| 202_K | 206_A | 1.198 | 0.94 |
| 224_A | 228_A | 1.191 | 0.93 |
| 484_K | 499_P | 1.175 | 0.93 |
| 215_V | 354_L | 1.174 | 0.93 |
| 435_V | 441_E | 1.174 | 0.93 |
| 294_K | 297_K | 1.172 | 0.93 |
| 222_W | 225_Y | 1.167 | 0.92 |
| 235_G | 238_G | 1.166 | 0.92 |
| 457_W | 462_L | 1.165 | 0.92 |
| 454_V | 457_W | 1.157 | 0.92 |
| 440_R | 447_G | 1.157 | 0.92 |
| 328_I | 331_T | 1.153 | 0.92 |
| 406_C | 416_P | 1.151 | 0.92 |
| 220_K | 224_A | 1.148 | 0.92 |
| 251_P | 254_W | 1.145 | 0.92 |
| 454_V | 459_E | 1.140 | 0.91 |
| 330_R | 372_K | 1.138 | 0.91 |
| 271_G | 425_V | 1.137 | 0.91 |
| 450_A | 458_A | 1.130 | 0.91 |
| 258_I | 348_I | 1.129 | 0.91 |
| 256_N | 353_P | 1.124 | 0.91 |
| 307_S | 348_I | 1.123 | 0.90 |
| 398_R | 473_P | 1.116 | 0.90 |
| 256_N | 354_L | 1.112 | 0.90 |
| 219_N | 322_E | 1.112 | 0.90 |
| 463_Y | 472_N | 1.109 | 0.90 |
| 205_A | 210_A | 1.102 | 0.89 |
| 304_R | 351_S | 1.099 | 0.89 |
| 478_G | 481_E | 1.098 | 0.89 |
| 222_W | 236_G | 1.098 | 0.89 |
| 445_H | 449_G | 1.096 | 0.89 |
| 220_K | 223_V | 1.096 | 0.89 |
| 212_F | 261_T | 1.093 | 0.89 |
| 466_N | 472_N | 1.085 | 0.88 |
| 238_G | 243_G | 1.082 | 0.88 |
| 450_A | 453_N | 1.077 | 0.88 |
| 439_V | 442_V | 1.074 | 0.88 |
| 301_Y | 304_R | 1.073 | 0.88 |
| 452_Q | 487_K | 1.069 | 0.87 |
| 327_E | 428_W | 1.068 | 0.87 |
| 395_G | 399_F | 1.067 | 0.87 |
| 289_A | 346_A | 1.067 | 0.87 |
| 205_A | 260_V | 1.057 | 0.87 |
| 467_Y | 472_N | 1.054 | 0.86 |
| 317_P | 334_C | 1.052 | 0.86 |
| 360_V | 367_F | 1.051 | 0.86 |
| 231_G | 238_G | 1.048 | 0.86 |
| 392_E | 395_G | 1.047 | 0.86 |
| 275_Y | 278_S | 1.040 | 0.85 |
| 215_V | 258_I | 1.036 | 0.85 |
| 485_W | 489_N | 1.033 | 0.85 |
| 251_P | 349_T | 1.024 | 0.84 |
| 412_L | 416_P | 1.024 | 0.84 |
| 337_P | 367_F | 1.021 | 0.84 |
| 288_I | 437_R | 1.015 | 0.83 |
| 287_Q | 291_Q | 1.015 | 0.83 |
| 492_V | 496_V | 1.013 | 0.83 |
| 257_A | 347_V | 1.012 | 0.83 |
| 208_L | 291_Q | 1.011 | 0.83 |
| 216_T | 323_C | 1.011 | 0.83 |
| 438_F | 441_E | 1.004 | 0.82 |
| 242_F | 245_N | 1.003 | 0.82 |
| 332_S | 386_D | 1.000 | 0.82 |
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 | |
| 1hfeL | 2 | 0.2942 | 98.4 | 0.942 | Contact Map |
| 3i9v9 | 2 | 0.2863 | 98.1 | 0.947 | Contact Map |
| 3gyxB | 6 | 0.2505 | 98 | 0.947 | Contact Map |
| 7fd1A | 1 | 0.2048 | 98 | 0.948 | Contact Map |
| 1h98A | 1 | 0.1491 | 98 | 0.948 | Contact Map |
| 2zvsA | 3 | 0.1471 | 97.9 | 0.949 | Contact Map |
| 1bc6A | 1 | 0.1491 | 97.9 | 0.949 | Contact Map |
| 1jb0C | 1 | 0.1571 | 97.9 | 0.949 | Contact Map |
| 2fdnA | 1 | 0.1093 | 97.9 | 0.95 | Contact Map |
| 3mm5B | 2 | 0.6243 | 97.8 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)