| 3rko-N |
| ID: | 1408345931 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 485 (471) | ||
| Sequences: | 5281 (3321.4) | ||
| Seq/Len: | 11.212 | ||
| Nf(neff/√len): | 153.0 |
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: 11.212).
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 |
| 70_D | 256_R | 5.162 | 1.00 |
| 118_L | 131_G | 4.755 | 1.00 |
| 293_N | 357_D | 3.777 | 1.00 |
| 158_K | 229_D | 3.633 | 1.00 |
| 339_G | 379_M | 3.409 | 1.00 |
| 332_G | 390_L | 3.153 | 1.00 |
| 231_Y | 239_S | 3.007 | 1.00 |
| 80_V | 120_A | 2.942 | 1.00 |
| 220_L | 310_L | 2.836 | 1.00 |
| 77_T | 121_N | 2.662 | 1.00 |
| 84_S | 113_A | 2.617 | 1.00 |
| 329_Y | 394_G | 2.606 | 1.00 |
| 231_Y | 246_S | 2.601 | 1.00 |
| 183_D | 188_A | 2.478 | 1.00 |
| 144_G | 156_S | 2.413 | 1.00 |
| 185_S | 188_A | 2.408 | 1.00 |
| 285_N | 304_S | 2.386 | 1.00 |
| 358_S | 361_S | 2.382 | 1.00 |
| 20_T | 44_G | 2.380 | 1.00 |
| 281_I | 417_G | 2.331 | 1.00 |
| 325_A | 401_V | 2.318 | 1.00 |
| 301_S | 424_Y | 2.202 | 1.00 |
| 289_L | 423_Y | 2.141 | 1.00 |
| 282_I | 417_G | 2.139 | 1.00 |
| 77_T | 117_I | 2.126 | 1.00 |
| 124_H | 184_L | 2.108 | 1.00 |
| 219_S | 227_T | 2.100 | 1.00 |
| 427_R | 431_S | 2.085 | 1.00 |
| 335_F | 463_L | 2.085 | 1.00 |
| 470_W | 473_P | 2.058 | 1.00 |
| 91_A | 105_F | 2.052 | 1.00 |
| 154_E | 158_K | 2.052 | 1.00 |
| 402_G | 411_V | 2.041 | 1.00 |
| 211_I | 215_G | 2.040 | 1.00 |
| 215_G | 220_L | 1.984 | 1.00 |
| 333_Y | 337_S | 1.969 | 1.00 |
| 369_R | 372_L | 1.963 | 1.00 |
| 356_A | 361_S | 1.950 | 1.00 |
| 292_T | 360_F | 1.912 | 1.00 |
| 220_L | 276_I | 1.912 | 1.00 |
| 312_A | 398_V | 1.887 | 1.00 |
| 294_I | 428_V | 1.877 | 1.00 |
| 277_A | 314_I | 1.873 | 1.00 |
| 173_G | 213_G | 1.854 | 1.00 |
| 115_G | 134_L | 1.845 | 1.00 |
| 173_G | 210_M | 1.803 | 1.00 |
| 462_L | 466_V | 1.774 | 1.00 |
| 70_D | 73_A | 1.753 | 1.00 |
| 73_A | 251_F | 1.749 | 1.00 |
| 247_K | 252_G | 1.735 | 1.00 |
| 124_H | 185_S | 1.733 | 1.00 |
| 298_L | 344_V | 1.692 | 1.00 |
| 122_A | 127_S | 1.682 | 1.00 |
| 128_L | 186_F | 1.665 | 1.00 |
| 236_A | 295_K | 1.659 | 1.00 |
| 291_Q | 296_R | 1.649 | 1.00 |
| 125_L | 189_L | 1.647 | 1.00 |
| 142_L | 238_V | 1.627 | 1.00 |
| 311_V | 414_V | 1.621 | 1.00 |
| 380_M | 425_Y | 1.616 | 1.00 |
| 211_I | 273_L | 1.607 | 1.00 |
| 123_N | 187_V | 1.591 | 1.00 |
| 229_D | 296_R | 1.583 | 1.00 |
| 377_T | 429_A | 1.575 | 1.00 |
| 140_F | 163_S | 1.570 | 1.00 |
| 246_S | 302_S | 1.567 | 1.00 |
| 255_M | 313_L | 1.566 | 1.00 |
| 337_S | 345_S | 1.557 | 1.00 |
| 227_T | 231_Y | 1.548 | 1.00 |
| 170_L | 213_G | 1.538 | 1.00 |
| 333_Y | 345_S | 1.536 | 1.00 |
| 467_L | 474_L | 1.534 | 1.00 |
| 81_L | 117_I | 1.533 | 1.00 |
| 399_L | 414_V | 1.526 | 1.00 |
| 377_T | 433_Y | 1.526 | 1.00 |
| 108_L | 141_G | 1.507 | 1.00 |
| 376_M | 380_M | 1.488 | 1.00 |
| 14_L | 77_T | 1.486 | 1.00 |
| 376_M | 433_Y | 1.481 | 1.00 |
| 271_V | 275_I | 1.480 | 1.00 |
| 180_Q | 206_G | 1.472 | 1.00 |
| 381_L | 386_I | 1.468 | 1.00 |
| 231_Y | 302_S | 1.465 | 1.00 |
| 328_V | 394_G | 1.461 | 1.00 |
| 329_Y | 332_G | 1.446 | 1.00 |
| 173_G | 206_G | 1.437 | 1.00 |
| 231_Y | 243_A | 1.437 | 1.00 |
| 277_A | 310_L | 1.427 | 1.00 |
| 285_N | 301_S | 1.427 | 1.00 |
| 315_A | 322_S | 1.421 | 1.00 |
| 249_A | 252_G | 1.416 | 1.00 |
| 143_V | 230_V | 1.412 | 1.00 |
| 305_H | 424_Y | 1.395 | 0.99 |
| 68_R | 123_N | 1.385 | 0.99 |
| 183_D | 189_L | 1.384 | 0.99 |
| 170_L | 174_M | 1.367 | 0.99 |
| 472_Q | 476_S | 1.361 | 0.99 |
| 292_T | 358_S | 1.359 | 0.99 |
| 125_L | 174_M | 1.353 | 0.99 |
| 161_I | 165_A | 1.335 | 0.99 |
| 277_A | 311_V | 1.333 | 0.99 |
| 312_A | 322_S | 1.328 | 0.99 |
| 21_V | 111_I | 1.328 | 0.99 |
| 285_N | 417_G | 1.322 | 0.99 |
| 374_A | 378_V | 1.316 | 0.99 |
| 129_F | 171_L | 1.315 | 0.99 |
| 155_A | 233_G | 1.306 | 0.99 |
| 128_L | 252_G | 1.304 | 0.99 |
| 15_L | 19_L | 1.299 | 0.99 |
| 216_F | 223_F | 1.292 | 0.99 |
| 309_L | 326_V | 1.282 | 0.99 |
| 395_K | 418_S | 1.280 | 0.99 |
| 110_L | 114_L | 1.279 | 0.99 |
| 83_A | 244_T | 1.275 | 0.99 |
| 247_K | 251_F | 1.275 | 0.99 |
| 83_A | 334_L | 1.275 | 0.99 |
| 116_G | 245_A | 1.273 | 0.99 |
| 88_C | 109_V | 1.272 | 0.99 |
| 129_F | 140_F | 1.266 | 0.99 |
| 73_A | 256_R | 1.265 | 0.99 |
| 221_V | 224_H | 1.258 | 0.99 |
| 374_A | 433_Y | 1.257 | 0.99 |
| 69_V | 121_N | 1.253 | 0.99 |
| 231_Y | 295_K | 1.252 | 0.99 |
| 363_R | 431_S | 1.244 | 0.98 |
| 292_T | 301_S | 1.244 | 0.98 |
| 308_Y | 398_V | 1.243 | 0.98 |
| 304_S | 421_G | 1.242 | 0.98 |
| 116_G | 135_I | 1.240 | 0.98 |
| 175_A | 179_A | 1.240 | 0.98 |
| 373_A | 429_A | 1.235 | 0.98 |
| 132_I | 170_L | 1.227 | 0.98 |
| 379_M | 464_V | 1.225 | 0.98 |
| 297_L | 359_L | 1.213 | 0.98 |
| 228_P | 300_Y | 1.201 | 0.98 |
| 66_L | 123_N | 1.200 | 0.98 |
| 304_S | 424_Y | 1.199 | 0.98 |
| 331_A | 474_L | 1.190 | 0.98 |
| 247_K | 250_I | 1.183 | 0.98 |
| 75_L | 331_A | 1.175 | 0.98 |
| 88_C | 106_Y | 1.174 | 0.98 |
| 248_I | 252_G | 1.172 | 0.98 |
| 378_V | 465_L | 1.171 | 0.98 |
| 336_S | 382_S | 1.167 | 0.97 |
| 239_S | 295_K | 1.159 | 0.97 |
| 466_V | 470_W | 1.159 | 0.97 |
| 330_L | 333_Y | 1.157 | 0.97 |
| 129_F | 167_S | 1.157 | 0.97 |
| 390_L | 464_V | 1.151 | 0.97 |
| 333_Y | 341_F | 1.147 | 0.97 |
| 243_A | 302_S | 1.146 | 0.97 |
| 274_A | 314_I | 1.145 | 0.97 |
| 378_V | 461_A | 1.143 | 0.97 |
| 281_I | 308_Y | 1.141 | 0.97 |
| 91_A | 94_W | 1.137 | 0.97 |
| 285_N | 424_Y | 1.137 | 0.97 |
| 312_A | 326_V | 1.135 | 0.97 |
| 366_F | 373_A | 1.133 | 0.97 |
| 468_G | 471_P | 1.132 | 0.97 |
| 371_I | 374_A | 1.129 | 0.97 |
| 228_P | 291_Q | 1.127 | 0.97 |
| 243_A | 337_S | 1.125 | 0.97 |
| 334_L | 345_S | 1.116 | 0.96 |
| 451_S | 454_G | 1.115 | 0.96 |
| 132_I | 249_A | 1.114 | 0.96 |
| 332_G | 394_G | 1.105 | 0.96 |
| 313_L | 326_V | 1.102 | 0.96 |
| 227_T | 230_V | 1.102 | 0.96 |
| 215_G | 276_I | 1.099 | 0.96 |
| 336_S | 391_G | 1.098 | 0.96 |
| 376_M | 428_V | 1.097 | 0.96 |
| 245_A | 249_A | 1.097 | 0.96 |
| 359_L | 432_L | 1.095 | 0.96 |
| 221_V | 283_F | 1.092 | 0.96 |
| 248_I | 251_F | 1.086 | 0.96 |
| 255_M | 326_V | 1.084 | 0.96 |
| 459_I | 463_L | 1.082 | 0.96 |
| 235_P | 295_K | 1.080 | 0.95 |
| 388_M | 469_V | 1.079 | 0.95 |
| 183_D | 186_F | 1.078 | 0.95 |
| 143_V | 242_L | 1.077 | 0.95 |
| 76_Y | 330_L | 1.074 | 0.95 |
| 342_G | 345_S | 1.072 | 0.95 |
| 383_L | 425_Y | 1.070 | 0.95 |
| 396_F | 400_A | 1.069 | 0.95 |
| 427_R | 430_V | 1.067 | 0.95 |
| 76_Y | 252_G | 1.067 | 0.95 |
| 390_L | 467_L | 1.065 | 0.95 |
| 363_R | 438_E | 1.063 | 0.95 |
| 178_Y | 184_L | 1.062 | 0.95 |
| 274_A | 410_L | 1.059 | 0.95 |
| 126_A | 184_L | 1.058 | 0.95 |
| 80_V | 116_G | 1.057 | 0.95 |
| 83_A | 241_F | 1.057 | 0.95 |
| 255_M | 323_M | 1.055 | 0.95 |
| 49_L | 78_G | 1.054 | 0.95 |
| 173_G | 209_L | 1.053 | 0.95 |
| 284_G | 307_G | 1.051 | 0.94 |
| 231_Y | 306_L | 1.050 | 0.94 |
| 151_R | 232_Q | 1.050 | 0.94 |
| 178_Y | 181_S | 1.047 | 0.94 |
| 79_L | 334_L | 1.047 | 0.94 |
| 288_A | 424_Y | 1.044 | 0.94 |
| 231_Y | 244_T | 1.041 | 0.94 |
| 249_A | 253_V | 1.040 | 0.94 |
| 231_Y | 355_D | 1.040 | 0.94 |
| 80_V | 113_A | 1.038 | 0.94 |
| 333_Y | 338_L | 1.037 | 0.94 |
| 322_S | 401_V | 1.035 | 0.94 |
| 302_S | 333_Y | 1.030 | 0.94 |
| 26_L | 29_A | 1.028 | 0.94 |
| 133_E | 217_K | 1.028 | 0.94 |
| 251_F | 330_L | 1.026 | 0.94 |
| 315_A | 402_G | 1.025 | 0.93 |
| 408_W | 412_G | 1.023 | 0.93 |
| 473_P | 476_S | 1.022 | 0.93 |
| 169_F | 212_V | 1.021 | 0.93 |
| 311_V | 410_L | 1.017 | 0.93 |
| 181_S | 189_L | 1.014 | 0.93 |
| 119_L | 132_I | 1.011 | 0.93 |
| 340_A | 344_V | 1.011 | 0.93 |
| 24_V | 40_L | 1.005 | 0.93 |
| 385_G | 395_K | 1.004 | 0.93 |
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 | |
| 3rkoN | 2 | 0.9753 | 100 | 0.127 | Contact Map |
| 3rkoM | 2 | 0.9505 | 100 | 0.245 | Contact Map |
| 4he8M | 2 | 0.9175 | 100 | 0.261 | Contact Map |
| 4he8L | 2 | 0.9505 | 100 | 0.264 | Contact Map |
| 4he8N | 2 | 0.8804 | 100 | 0.264 | Contact Map |
| 3rkoL | 2 | 0.9526 | 100 | 0.283 | Contact Map |
| 4he8K | 2 | 0.1918 | 54 | 0.965 | Contact Map |
| 3rkoK | 2 | 0.2 | 44.3 | 0.967 | Contact Map |
| 3arcX | 2 | 0.0784 | 4 | 0.98 | Contact Map |
| 1fftB | 2 | 0.1938 | 1.8 | 0.983 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)