| Muscle_without_TAT |
| ID: | 1416338371 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 503 (268) | ||
| Sequences: | 1740 (1101.7) | ||
| Seq/Len: | 6.493 | ||
| Nf(neff/√len): | 67.3 |
HHblits Results: (2013_03)
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: 6.493).
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 |
| 336_A | 343_V | 3.374 | 1.00 |
| 204_M | 207_D | 2.906 | 1.00 |
| 375_A | 383_I | 2.477 | 1.00 |
| 255_D | 353_P | 2.432 | 1.00 |
| 372_K | 376_Q | 2.429 | 1.00 |
| 317_P | 333_N | 2.418 | 1.00 |
| 260_V | 346_A | 2.249 | 1.00 |
| 202_K | 215_V | 2.233 | 1.00 |
| 332_S | 401_T | 2.227 | 1.00 |
| 198_S | 215_V | 2.209 | 1.00 |
| 254_W | 349_T | 2.201 | 1.00 |
| 261_T | 345_P | 2.181 | 1.00 |
| 274_N | 344_R | 2.103 | 1.00 |
| 259_L | 347_V | 2.074 | 1.00 |
| 402_N | 405_K | 2.073 | 1.00 |
| 212_F | 336_A | 1.989 | 1.00 |
| 202_K | 357_D | 1.937 | 1.00 |
| 258_I | 350_T | 1.891 | 1.00 |
| 261_T | 343_V | 1.889 | 1.00 |
| 198_S | 355_A | 1.888 | 1.00 |
| 382_A | 405_K | 1.819 | 1.00 |
| 326_G | 334_C | 1.808 | 1.00 |
| 339_F | 343_V | 1.775 | 1.00 |
| 198_S | 202_K | 1.742 | 1.00 |
| 313_D | 349_T | 1.729 | 1.00 |
| 377_V | 425_V | 1.719 | 1.00 |
| 240_R | 243_G | 1.666 | 1.00 |
| 215_V | 256_N | 1.663 | 1.00 |
| 235_G | 238_G | 1.606 | 1.00 |
| 259_L | 323_C | 1.585 | 1.00 |
| 215_V | 354_L | 1.577 | 0.99 |
| 337_P | 360_V | 1.561 | 0.99 |
| 325_M | 334_C | 1.536 | 0.99 |
| 239_G | 244_I | 1.520 | 0.99 |
| 237_T | 242_F | 1.500 | 0.99 |
| 211_T | 263_T | 1.490 | 0.99 |
| 331_T | 383_I | 1.487 | 0.99 |
| 198_S | 357_D | 1.478 | 0.99 |
| 234_G | 238_G | 1.451 | 0.99 |
| 237_T | 240_R | 1.450 | 0.99 |
| 317_P | 328_I | 1.443 | 0.99 |
| 238_G | 242_F | 1.431 | 0.99 |
| 422_C | 426_C | 1.430 | 0.99 |
| 256_N | 354_L | 1.424 | 0.99 |
| 332_S | 383_I | 1.423 | 0.99 |
| 300_G | 351_S | 1.408 | 0.99 |
| 234_G | 242_F | 1.407 | 0.99 |
| 235_G | 242_F | 1.392 | 0.98 |
| 237_T | 244_I | 1.389 | 0.98 |
| 235_G | 240_R | 1.387 | 0.98 |
| 201_I | 258_I | 1.367 | 0.98 |
| 275_Y | 278_S | 1.358 | 0.98 |
| 293_V | 348_I | 1.355 | 0.98 |
| 205_A | 213_V | 1.326 | 0.98 |
| 232_G | 235_G | 1.322 | 0.98 |
| 383_I | 401_T | 1.315 | 0.98 |
| 328_I | 334_C | 1.312 | 0.97 |
| 287_Q | 291_Q | 1.294 | 0.97 |
| 316_V | 347_V | 1.278 | 0.97 |
| 235_G | 245_N | 1.273 | 0.97 |
| 327_E | 428_W | 1.273 | 0.97 |
| 217_P | 256_N | 1.269 | 0.97 |
| 204_M | 208_L | 1.266 | 0.97 |
| 419_C | 426_C | 1.258 | 0.97 |
| 327_E | 367_F | 1.256 | 0.96 |
| 235_G | 239_G | 1.250 | 0.96 |
| 330_R | 372_K | 1.250 | 0.96 |
| 232_G | 237_T | 1.250 | 0.96 |
| 419_C | 422_C | 1.249 | 0.96 |
| 234_G | 237_T | 1.246 | 0.96 |
| 212_F | 338_D | 1.237 | 0.96 |
| 407_R | 410_W | 1.237 | 0.96 |
| 238_G | 241_G | 1.234 | 0.96 |
| 217_P | 322_E | 1.232 | 0.96 |
| 242_F | 245_N | 1.222 | 0.96 |
| 212_F | 261_T | 1.219 | 0.96 |
| 237_T | 243_G | 1.216 | 0.96 |
| 235_G | 243_G | 1.200 | 0.95 |
| 239_G | 242_F | 1.199 | 0.95 |
| 257_A | 319_I | 1.198 | 0.95 |
| 202_K | 206_A | 1.171 | 0.94 |
| 199_Q | 203_R | 1.167 | 0.94 |
| 318_G | 321_A | 1.166 | 0.94 |
| 241_G | 244_I | 1.166 | 0.94 |
| 315_P | 318_G | 1.164 | 0.94 |
| 451_S | 454_V | 1.150 | 0.93 |
| 246_T | 250_I | 1.149 | 0.93 |
| 385_Y | 394_Y | 1.147 | 0.93 |
| 406_C | 419_C | 1.145 | 0.93 |
| 215_V | 357_D | 1.145 | 0.93 |
| 236_G | 242_F | 1.143 | 0.93 |
| 236_G | 244_I | 1.141 | 0.93 |
| 230_L | 245_N | 1.137 | 0.93 |
| 273_P | 277_D | 1.135 | 0.93 |
| 341_G | 423_I | 1.133 | 0.93 |
| 372_K | 375_A | 1.123 | 0.92 |
| 230_L | 234_G | 1.118 | 0.92 |
| 301_Y | 350_T | 1.114 | 0.92 |
| 257_A | 349_T | 1.111 | 0.92 |
| 229_P | 233_L | 1.109 | 0.92 |
| 200_L | 299_L | 1.109 | 0.92 |
| 296_L | 303_A | 1.102 | 0.91 |
| 330_R | 375_A | 1.101 | 0.91 |
| 213_V | 260_V | 1.095 | 0.91 |
| 215_V | 258_I | 1.095 | 0.91 |
| 260_V | 348_I | 1.090 | 0.91 |
| 272_D | 278_S | 1.088 | 0.91 |
| 236_G | 240_R | 1.086 | 0.91 |
| 301_Y | 353_P | 1.085 | 0.91 |
| 230_L | 236_G | 1.083 | 0.90 |
| 232_G | 242_F | 1.081 | 0.90 |
| 238_G | 244_I | 1.080 | 0.90 |
| 377_V | 421_A | 1.076 | 0.90 |
| 211_T | 339_F | 1.075 | 0.90 |
| 297_K | 351_S | 1.074 | 0.90 |
| 240_R | 244_I | 1.073 | 0.90 |
| 418_G | 423_I | 1.072 | 0.90 |
| 232_G | 245_N | 1.065 | 0.89 |
| 423_I | 429_T | 1.064 | 0.89 |
| 228_A | 231_G | 1.062 | 0.89 |
| 257_A | 347_V | 1.061 | 0.89 |
| 233_L | 237_T | 1.054 | 0.89 |
| 295_F | 299_L | 1.053 | 0.89 |
| 222_W | 226_S | 1.048 | 0.88 |
| 341_G | 429_T | 1.047 | 0.88 |
| 229_P | 232_G | 1.042 | 0.88 |
| 305_W | 348_I | 1.041 | 0.88 |
| 454_V | 458_A | 1.039 | 0.88 |
| 275_Y | 424_S | 1.035 | 0.88 |
| 330_R | 369_S | 1.033 | 0.87 |
| 231_G | 234_G | 1.033 | 0.87 |
| 244_I | 247_P | 1.031 | 0.87 |
| 327_E | 330_R | 1.029 | 0.87 |
| 216_T | 323_C | 1.026 | 0.87 |
| 316_V | 345_P | 1.024 | 0.87 |
| 213_V | 258_I | 1.021 | 0.87 |
| 231_G | 238_G | 1.021 | 0.87 |
| 239_G | 243_G | 1.021 | 0.87 |
| 217_P | 356_A | 1.020 | 0.87 |
| 259_L | 319_I | 1.019 | 0.87 |
| 204_M | 295_F | 1.017 | 0.86 |
| 238_G | 243_G | 1.013 | 0.86 |
| 205_A | 210_A | 1.013 | 0.86 |
| 229_P | 236_G | 1.010 | 0.86 |
| 319_I | 347_V | 1.004 | 0.85 |
| 230_L | 235_G | 1.003 | 0.85 |
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 | 0.2783 | 98.3 | 0.926 | Contact Map |
| 7fd1A | 1 | 0.2068 | 98.1 | 0.93 | Contact Map |
| 1bc6A | 1 | 0.1491 | 98 | 0.932 | Contact Map |
| 1h98A | 1 | 0.1491 | 97.9 | 0.933 | Contact Map |
| 2zvsA | 3 | 0.1471 | 97.9 | 0.934 | Contact Map |
| 2fdnA | 1 | 0.1093 | 97.9 | 0.934 | Contact Map |
| 2fgoA | 1 | 0.1491 | 97.9 | 0.934 | Contact Map |
| 3eunA | 1 | 0.1491 | 97.9 | 0.934 | Contact Map |
| 3i9v9 | 2 | 0.2704 | 97.9 | 0.934 | Contact Map |
| 1xerA | 1 | 0.2028 | 97.8 | 0.936 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)