| nd5aln_enrich |
| ID: | 1499526238 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 516 (509) | ||
| Sequences: | 5820 (2641.9) | ||
| Seq/Len: | 11.434 | ||
| Nf(neff/√len): | 117.1 |
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: 11.434).
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 |
| 233_I | 288_I | 3.981 | 1.00 |
| 84_L | 199_F | 3.795 | 1.00 |
| 234_I | 275_S | 3.660 | 1.00 |
| 213_G | 250_G | 3.253 | 1.00 |
| 247_V | 344_T | 3.193 | 1.00 |
| 37_M | 80_T | 2.952 | 1.00 |
| 163_F | 215_I | 2.878 | 1.00 |
| 285_E | 290_K | 2.783 | 1.00 |
| 103_G | 113_A | 2.737 | 1.00 |
| 302_T | 364_L | 2.728 | 1.00 |
| 37_M | 76_L | 2.709 | 1.00 |
| 30_D | 198_R | 2.685 | 1.00 |
| 309_C | 355_S | 2.660 | 1.00 |
| 77_I | 90_G | 2.568 | 1.00 |
| 115_Q | 171_S | 2.469 | 1.00 |
| 53_W | 379_N | 2.444 | 1.00 |
| 288_I | 362_T | 2.433 | 1.00 |
| 118_Y | 167_P | 2.409 | 1.00 |
| 197_V | 258_F | 2.381 | 1.00 |
| 445_F | 450_G | 2.377 | 1.00 |
| 222_I | 450_G | 2.361 | 1.00 |
| 279_I | 286_Q | 2.354 | 1.00 |
| 84_L | 144_F | 2.352 | 1.00 |
| 481_L | 484_T | 2.345 | 1.00 |
| 81_A | 86_Q | 2.303 | 1.00 |
| 306_I | 359_I | 2.264 | 1.00 |
| 225_L | 353_I | 2.209 | 1.00 |
| 277_S | 378_N | 2.198 | 1.00 |
| 346_T | 350_L | 2.161 | 1.00 |
| 356_T | 360_F | 2.154 | 1.00 |
| 94_V | 188_M | 2.144 | 1.00 |
| 228_N | 289_R | 2.116 | 1.00 |
| 39_V | 265_A | 2.076 | 1.00 |
| 260_H | 323_S | 2.073 | 1.00 |
| 226_T | 446_S | 2.025 | 1.00 |
| 304_A | 390_L | 2.014 | 1.00 |
| 140_D | 143_I | 2.012 | 1.00 |
| 295_F | 302_T | 2.009 | 1.00 |
| 44_T | 72_L | 1.938 | 1.00 |
| 249_I | 257_A | 1.927 | 1.00 |
| 263_T | 319_T | 1.924 | 1.00 |
| 301_T | 377_E | 1.917 | 1.00 |
| 270_M | 308_G | 1.898 | 1.00 |
| 107_R | 110_A | 1.892 | 1.00 |
| 280_H | 284_N | 1.891 | 1.00 |
| 310_L | 315_M | 1.882 | 1.00 |
| 209_T | 250_G | 1.866 | 1.00 |
| 328_I | 348_T | 1.837 | 1.00 |
| 218_L | 347_A | 1.818 | 1.00 |
| 90_G | 93_G | 1.805 | 1.00 |
| 196_L | 203_M | 1.796 | 1.00 |
| 288_I | 361_F | 1.747 | 1.00 |
| 298_L | 301_T | 1.741 | 1.00 |
| 193_I | 246_M | 1.735 | 1.00 |
| 213_G | 243_G | 1.731 | 1.00 |
| 60_Y | 63_Q | 1.728 | 1.00 |
| 128_A | 151_G | 1.724 | 1.00 |
| 40_S | 79_V | 1.710 | 1.00 |
| 348_T | 424_M | 1.705 | 1.00 |
| 328_I | 344_T | 1.695 | 1.00 |
| 114_L | 117_L | 1.688 | 1.00 |
| 305_L | 358_I | 1.682 | 1.00 |
| 222_I | 350_L | 1.671 | 1.00 |
| 241_Q | 351_T | 1.670 | 1.00 |
| 39_V | 262_C | 1.663 | 1.00 |
| 45_W | 49_E | 1.649 | 1.00 |
| 138_T | 143_I | 1.636 | 1.00 |
| 214_A | 340_A | 1.635 | 1.00 |
| 325_D | 329_E | 1.625 | 1.00 |
| 218_L | 343_L | 1.617 | 1.00 |
| 281_N | 298_L | 1.613 | 1.00 |
| 342_L | 346_T | 1.606 | 1.00 |
| 421_A | 425_T | 1.600 | 1.00 |
| 74_T | 93_G | 1.598 | 1.00 |
| 355_S | 358_I | 1.594 | 1.00 |
| 380_P | 384_N | 1.575 | 1.00 |
| 125_G | 154_L | 1.574 | 1.00 |
| 210_L | 247_V | 1.565 | 1.00 |
| 158_G | 165_L | 1.560 | 1.00 |
| 150_M | 154_L | 1.558 | 1.00 |
| 132_W | 148_P | 1.540 | 1.00 |
| 307_I | 390_L | 1.525 | 1.00 |
| 282_L | 291_M | 1.524 | 1.00 |
| 309_C | 359_I | 1.514 | 1.00 |
| 274_C | 304_A | 1.512 | 1.00 |
| 70_L | 97_M | 1.496 | 1.00 |
| 53_W | 381_L | 1.493 | 1.00 |
| 270_M | 386_I | 1.484 | 1.00 |
| 32_F | 258_F | 1.476 | 1.00 |
| 251_L | 331_A | 1.474 | 1.00 |
| 28_K | 31_Y | 1.452 | 1.00 |
| 85_F | 139_W | 1.448 | 1.00 |
| 312_L | 355_S | 1.446 | 1.00 |
| 391_I | 395_F | 1.442 | 1.00 |
| 302_T | 359_I | 1.429 | 1.00 |
| 415_L | 419_L | 1.426 | 1.00 |
| 221_A | 347_A | 1.408 | 1.00 |
| 300_F | 387_K | 1.406 | 0.99 |
| 129_S | 155_A | 1.404 | 0.99 |
| 215_I | 343_L | 1.404 | 0.99 |
| 87_L | 195_L | 1.400 | 0.99 |
| 196_L | 249_I | 1.393 | 0.99 |
| 228_N | 287_D | 1.390 | 0.99 |
| 30_D | 33_S | 1.388 | 0.99 |
| 359_I | 364_L | 1.375 | 0.99 |
| 149_L | 202_L | 1.371 | 0.99 |
| 132_W | 135_N | 1.368 | 0.99 |
| 41_L | 76_L | 1.367 | 0.99 |
| 280_H | 376_N | 1.364 | 0.99 |
| 126_L | 195_L | 1.363 | 0.99 |
| 229_D | 286_Q | 1.355 | 0.99 |
| 300_F | 383_I | 1.351 | 0.99 |
| 52_M | 381_L | 1.350 | 0.99 |
| 347_A | 350_L | 1.343 | 0.99 |
| 196_L | 246_M | 1.309 | 0.99 |
| 40_S | 44_T | 1.307 | 0.99 |
| 149_L | 203_M | 1.296 | 0.99 |
| 219_F | 450_G | 1.289 | 0.99 |
| 157_A | 212_L | 1.276 | 0.99 |
| 369_F | 375_I | 1.272 | 0.99 |
| 74_T | 97_M | 1.267 | 0.99 |
| 498_G | 503_Y | 1.263 | 0.99 |
| 497_Q | 502_L | 1.261 | 0.99 |
| 426_T | 430_I | 1.256 | 0.99 |
| 197_V | 249_I | 1.256 | 0.99 |
| 319_T | 396_A | 1.256 | 0.99 |
| 49_E | 384_N | 1.255 | 0.99 |
| 233_I | 361_F | 1.255 | 0.99 |
| 53_W | 382_L | 1.243 | 0.98 |
| 309_C | 313_T | 1.237 | 0.98 |
| 150_M | 208_T | 1.235 | 0.98 |
| 277_S | 301_T | 1.233 | 0.98 |
| 16_V | 23_L | 1.226 | 0.98 |
| 14_H | 24_T | 1.226 | 0.98 |
| 163_F | 219_F | 1.221 | 0.98 |
| 392_G | 396_A | 1.221 | 0.98 |
| 430_I | 434_E | 1.218 | 0.98 |
| 215_I | 339_W | 1.216 | 0.98 |
| 14_H | 17_T | 1.213 | 0.98 |
| 352_A | 425_T | 1.211 | 0.98 |
| 383_I | 387_K | 1.210 | 0.98 |
| 141_Q | 144_F | 1.210 | 0.98 |
| 47_I | 273_L | 1.209 | 0.98 |
| 153_V | 208_T | 1.186 | 0.98 |
| 46_S | 269_A | 1.183 | 0.98 |
| 304_A | 387_K | 1.180 | 0.98 |
| 50_F | 284_N | 1.175 | 0.98 |
| 14_H | 22_K | 1.174 | 0.98 |
| 120_R | 123_D | 1.173 | 0.98 |
| 210_L | 251_L | 1.171 | 0.98 |
| 51_S | 64_F | 1.166 | 0.97 |
| 329_E | 418_K | 1.165 | 0.97 |
| 244_L | 348_T | 1.160 | 0.97 |
| 42_F | 46_S | 1.159 | 0.97 |
| 33_S | 194_F | 1.156 | 0.97 |
| 483_K | 486_A | 1.152 | 0.97 |
| 356_T | 429_F | 1.152 | 0.97 |
| 390_L | 393_S | 1.151 | 0.97 |
| 428_G | 432_A | 1.141 | 0.97 |
| 157_A | 250_G | 1.139 | 0.97 |
| 273_L | 386_I | 1.135 | 0.97 |
| 387_K | 391_I | 1.133 | 0.97 |
| 61_I | 65_F | 1.130 | 0.97 |
| 303_T | 306_I | 1.128 | 0.97 |
| 297_A | 375_I | 1.126 | 0.97 |
| 355_S | 359_I | 1.122 | 0.97 |
| 266_F | 396_A | 1.121 | 0.97 |
| 248_T | 327_I | 1.121 | 0.97 |
| 267_F | 320_G | 1.120 | 0.96 |
| 127_L | 131_A | 1.118 | 0.96 |
| 430_I | 433_F | 1.114 | 0.96 |
| 448_L | 451_Y | 1.109 | 0.96 |
| 316_P | 322_Y | 1.105 | 0.96 |
| 29_M | 80_T | 1.105 | 0.96 |
| 108_T | 174_E | 1.103 | 0.96 |
| 217_T | 347_A | 1.101 | 0.96 |
| 214_A | 343_L | 1.099 | 0.96 |
| 156_A | 246_M | 1.098 | 0.96 |
| 129_S | 133_F | 1.098 | 0.96 |
| 385_P | 388_R | 1.093 | 0.96 |
| 449_L | 453_P | 1.091 | 0.96 |
| 449_L | 454_T | 1.089 | 0.96 |
| 35_M | 258_F | 1.087 | 0.96 |
| 153_V | 209_T | 1.086 | 0.96 |
| 159_K | 231_K | 1.086 | 0.96 |
| 130_M | 139_W | 1.086 | 0.96 |
| 167_P | 456_M | 1.086 | 0.96 |
| 81_A | 87_L | 1.085 | 0.96 |
| 262_C | 400_L | 1.085 | 0.96 |
| 133_F | 148_P | 1.080 | 0.95 |
| 304_A | 386_I | 1.079 | 0.95 |
| 50_F | 273_L | 1.078 | 0.95 |
| 35_M | 262_C | 1.075 | 0.95 |
| 280_H | 382_L | 1.072 | 0.95 |
| 104_W | 107_R | 1.072 | 0.95 |
| 288_I | 358_I | 1.066 | 0.95 |
| 380_P | 387_K | 1.065 | 0.95 |
| 260_H | 267_F | 1.064 | 0.95 |
| 222_I | 446_S | 1.064 | 0.95 |
| 174_E | 232_K | 1.063 | 0.95 |
| 286_Q | 289_R | 1.063 | 0.95 |
| 378_N | 383_I | 1.062 | 0.95 |
| 351_T | 354_Y | 1.062 | 0.95 |
| 106_G | 110_A | 1.060 | 0.95 |
| 211_C | 215_I | 1.057 | 0.95 |
| 306_I | 364_L | 1.055 | 0.95 |
| 424_M | 428_G | 1.054 | 0.95 |
| 166_H | 452_F | 1.052 | 0.95 |
| 277_S | 377_E | 1.051 | 0.94 |
| 48_M | 69_L | 1.049 | 0.94 |
| 68_L | 179_V | 1.048 | 0.94 |
| 282_L | 285_E | 1.045 | 0.94 |
| 183_L | 190_V | 1.044 | 0.94 |
| 384_N | 387_K | 1.044 | 0.94 |
| 210_L | 340_A | 1.041 | 0.94 |
| 26_S | 82_N | 1.040 | 0.94 |
| 263_T | 323_S | 1.034 | 0.94 |
| 240_S | 351_T | 1.034 | 0.94 |
| 278_I | 305_L | 1.031 | 0.94 |
| 473_D | 476_W | 1.028 | 0.94 |
| 50_F | 280_H | 1.028 | 0.94 |
| 293_G | 367_P | 1.028 | 0.94 |
| 309_C | 312_L | 1.026 | 0.94 |
| 306_I | 310_L | 1.025 | 0.93 |
| 164_G | 239_S | 1.023 | 0.93 |
| 234_I | 355_S | 1.019 | 0.93 |
| 84_L | 133_F | 1.018 | 0.93 |
| 71_F | 75_M | 1.017 | 0.93 |
| 259_L | 263_T | 1.013 | 0.93 |
| 427_L | 431_L | 1.012 | 0.93 |
| 326_P | 329_E | 1.012 | 0.93 |
| 464_L | 467_S | 1.012 | 0.93 |
| 289_R | 361_F | 1.011 | 0.93 |
| 33_S | 80_T | 1.011 | 0.93 |
| 199_F | 203_M | 1.007 | 0.93 |
| 332_T | 341_L | 1.006 | 0.93 |
| 110_A | 174_E | 1.005 | 0.93 |
| 259_L | 323_S | 1.005 | 0.93 |
| 496_Q | 499_L | 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 | |
| 3rkoL | 2 | 0.9884 | 100 | 0.295 | Contact Map |
| 4he8L | 2 | 0.9845 | 100 | 0.297 | Contact Map |
| 3rkoM | 2 | 0.8023 | 100 | 0.476 | Contact Map |
| 4he8M | 2 | 0.7752 | 100 | 0.49 | Contact Map |
| 3rkoN | 2 | 0.7849 | 100 | 0.504 | Contact Map |
| 4he8N | 2 | 0.7558 | 100 | 0.515 | Contact Map |
| 4he8K | 2 | 0.1725 | 7.6 | 0.981 | Contact Map |
| 3rkoK | 2 | 0.1802 | 6.8 | 0.982 | Contact Map |
| 1rklA | 1 | 0.0698 | 1.3 | 0.988 | Contact Map |
| 2k3cA | 1 | 0.0601 | 1 | 0.989 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)