| lielsi |
| ID: | 1497214472 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 686 (639) | ||
| Sequences: | 2709 (2098.4) | ||
| Seq/Len: | 4.239 | ||
| Nf(neff/√len): | 83.0 |
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: 4.239).
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 |
| 181_K | 187_L | 4.877 | 1.00 |
| 625_N | 628_E | 4.655 | 1.00 |
| 29_K | 32_E | 4.557 | 1.00 |
| 483_E | 486_N | 4.513 | 1.00 |
| 362_E | 365_Q | 4.225 | 1.00 |
| 220_E | 223_K | 4.155 | 1.00 |
| 570_Q | 573_A | 4.050 | 1.00 |
| 354_G | 370_F | 4.013 | 1.00 |
| 63_E | 66_R | 3.837 | 1.00 |
| 136_K | 139_K | 3.778 | 1.00 |
| 396_N | 399_E | 3.699 | 1.00 |
| 258_N | 261_F | 3.620 | 1.00 |
| 535_D | 538_A | 3.499 | 1.00 |
| 476_V | 491_F | 3.114 | 1.00 |
| 584_D | 587_E | 3.104 | 1.00 |
| 37_F | 53_L | 3.026 | 1.00 |
| 388_G | 404_L | 2.799 | 1.00 |
| 441_R | 454_D | 2.597 | 1.00 |
| 527_G | 543_W | 2.517 | 1.00 |
| 212_A | 228_Y | 2.446 | 1.00 |
| 351_Y | 386_E | 2.423 | 1.00 |
| 215_Y | 223_K | 2.335 | 1.00 |
| 433_G | 459_F | 2.215 | 1.00 |
| 316_V | 319_N | 2.179 | 1.00 |
| 391_A | 399_E | 2.179 | 1.00 |
| 353_R | 369_F | 2.169 | 1.00 |
| 456_I | 475_T | 2.161 | 1.00 |
| 357_F | 365_Q | 2.152 | 1.00 |
| 225_A | 245_L | 2.115 | 1.00 |
| 58_Y | 66_R | 1.983 | 1.00 |
| 617_G | 636_A | 1.964 | 1.00 |
| 562_A | 578_Y | 1.949 | 1.00 |
| 34_E | 54_Y | 1.932 | 1.00 |
| 189_I | 211_I | 1.922 | 1.00 |
| 162_G | 192_Y | 1.911 | 1.00 |
| 165_H | 181_K | 1.906 | 1.00 |
| 432_V | 436_Y | 1.902 | 1.00 |
| 387_L | 391_A | 1.901 | 1.00 |
| 55_G | 71_L | 1.873 | 1.00 |
| 565_F | 573_A | 1.853 | 1.00 |
| 31_F | 61_V | 1.826 | 1.00 |
| 211_I | 215_Y | 1.819 | 1.00 |
| 246_L | 266_H | 1.809 | 1.00 |
| 225_A | 252_M | 1.770 | 0.99 |
| 573_A | 576_G | 1.767 | 0.99 |
| 126_T | 129_A | 1.747 | 0.99 |
| 372_K | 375_T | 1.740 | 0.99 |
| 34_E | 58_Y | 1.737 | 0.99 |
| 158_Y | 191_F | 1.732 | 0.99 |
| 51_L | 70_K | 1.722 | 0.99 |
| 630_L | 654_K | 1.715 | 0.99 |
| 540_L | 564_A | 1.694 | 0.99 |
| 225_A | 229_N | 1.684 | 0.99 |
| 193_K | 211_I | 1.679 | 0.99 |
| 34_E | 61_V | 1.664 | 0.99 |
| 565_F | 577_N | 1.663 | 0.99 |
| 30_F | 57_E | 1.648 | 0.99 |
| 617_G | 633_Y | 1.646 | 0.99 |
| 616_I | 620_Y | 1.633 | 0.99 |
| 38_A | 54_Y | 1.622 | 0.99 |
| 530_D | 538_A | 1.619 | 0.99 |
| 358_A | 370_F | 1.604 | 0.99 |
| 537_A | 568_T | 1.597 | 0.99 |
| 527_G | 546_F | 1.596 | 0.99 |
| 211_I | 227_F | 1.594 | 0.99 |
| 205_E | 231_I | 1.586 | 0.99 |
| 209_A | 244_G | 1.582 | 0.99 |
| 187_L | 190_N | 1.582 | 0.99 |
| 478_K | 486_N | 1.580 | 0.99 |
| 391_A | 403_L | 1.577 | 0.99 |
| 620_Y | 628_E | 1.576 | 0.99 |
| 182_Y | 214_I | 1.568 | 0.99 |
| 367_R | 390_N | 1.559 | 0.98 |
| 252_M | 258_N | 1.548 | 0.98 |
| 527_G | 542_E | 1.545 | 0.98 |
| 634_W | 638_E | 1.534 | 0.98 |
| 523_R | 542_E | 1.534 | 0.98 |
| 34_E | 57_E | 1.529 | 0.98 |
| 561_K | 565_F | 1.525 | 0.98 |
| 617_G | 632_H | 1.517 | 0.98 |
| 165_H | 187_L | 1.511 | 0.98 |
| 161_L | 165_H | 1.499 | 0.98 |
| 189_I | 214_I | 1.496 | 0.98 |
| 613_Y | 632_H | 1.491 | 0.98 |
| 249_Y | 265_H | 1.486 | 0.98 |
| 106_Q | 119_V | 1.475 | 0.98 |
| 371_E | 387_L | 1.472 | 0.97 |
| 456_I | 478_K | 1.468 | 0.97 |
| 476_V | 490_G | 1.458 | 0.97 |
| 145_V | 161_L | 1.452 | 0.97 |
| 406_E | 545_G | 1.440 | 0.97 |
| 350_Y | 369_F | 1.432 | 0.97 |
| 384_S | 403_L | 1.430 | 0.97 |
| 24_E | 29_K | 1.423 | 0.97 |
| 367_R | 387_L | 1.415 | 0.97 |
| 229_N | 245_L | 1.414 | 0.97 |
| 540_L | 565_F | 1.412 | 0.97 |
| 230_K | 233_E | 1.411 | 0.97 |
| 194_Q | 197_T | 1.410 | 0.97 |
| 367_R | 391_A | 1.400 | 0.96 |
| 40_G | 50_Y | 1.400 | 0.96 |
| 635_K | 639_T | 1.399 | 0.96 |
| 562_A | 581_V | 1.391 | 0.96 |
| 564_A | 568_T | 1.388 | 0.96 |
| 232_V | 242_Q | 1.383 | 0.96 |
| 57_E | 61_V | 1.379 | 0.96 |
| 228_Y | 244_G | 1.379 | 0.96 |
| 493_K | 496_S | 1.378 | 0.96 |
| 475_T | 478_K | 1.375 | 0.96 |
| 392_I | 404_L | 1.373 | 0.96 |
| 225_A | 248_T | 1.369 | 0.96 |
| 405_N | 432_V | 1.360 | 0.95 |
| 391_A | 396_N | 1.360 | 0.95 |
| 462_R | 472_A | 1.356 | 0.95 |
| 540_L | 568_T | 1.354 | 0.95 |
| 478_K | 483_E | 1.353 | 0.95 |
| 182_Y | 221_F | 1.340 | 0.95 |
| 461_G | 464_I | 1.336 | 0.95 |
| 354_G | 373_A | 1.331 | 0.95 |
| 401_D | 405_N | 1.326 | 0.95 |
| 654_K | 658_F | 1.324 | 0.95 |
| 456_I | 481_S | 1.323 | 0.95 |
| 613_Y | 635_K | 1.320 | 0.94 |
| 55_G | 70_K | 1.313 | 0.94 |
| 401_D | 439_K | 1.312 | 0.94 |
| 41_E | 51_L | 1.309 | 0.94 |
| 530_D | 542_E | 1.306 | 0.94 |
| 433_G | 562_A | 1.301 | 0.94 |
| 544_S | 561_K | 1.292 | 0.94 |
| 357_F | 369_F | 1.291 | 0.94 |
| 261_F | 264_N | 1.286 | 0.93 |
| 347_A | 373_A | 1.285 | 0.93 |
| 540_L | 544_S | 1.283 | 0.93 |
| 146_M | 149_E | 1.276 | 0.93 |
| 380_H | 383_A | 1.274 | 0.93 |
| 636_A | 650_A | 1.274 | 0.93 |
| 326_L | 493_K | 1.273 | 0.93 |
| 399_E | 402_K | 1.266 | 0.93 |
| 271_N | 375_T | 1.266 | 0.93 |
| 432_V | 458_E | 1.261 | 0.92 |
| 365_Q | 368_R | 1.255 | 0.92 |
| 526_K | 542_E | 1.251 | 0.92 |
| 472_A | 490_G | 1.249 | 0.92 |
| 401_D | 435_I | 1.247 | 0.92 |
| 408_L | 429_Q | 1.247 | 0.92 |
| 189_I | 193_K | 1.247 | 0.92 |
| 162_G | 191_F | 1.245 | 0.92 |
| 58_Y | 70_K | 1.242 | 0.92 |
| 628_E | 631_K | 1.237 | 0.92 |
| 141_G | 161_L | 1.233 | 0.91 |
| 196_Y | 208_T | 1.226 | 0.91 |
| 406_E | 409_K | 1.219 | 0.91 |
| 152_T | 378_P | 1.217 | 0.91 |
| 540_L | 561_K | 1.212 | 0.90 |
| 486_N | 489_E | 1.211 | 0.90 |
| 617_G | 657_M | 1.208 | 0.90 |
| 236_P | 296_K | 1.205 | 0.90 |
| 54_Y | 58_Y | 1.203 | 0.90 |
| 208_T | 227_F | 1.201 | 0.90 |
| 454_D | 457_T | 1.191 | 0.89 |
| 616_I | 632_H | 1.189 | 0.89 |
| 388_G | 403_L | 1.188 | 0.89 |
| 635_K | 638_E | 1.182 | 0.89 |
| 139_K | 142_A | 1.181 | 0.89 |
| 263_I | 267_R | 1.180 | 0.89 |
| 211_I | 353_R | 1.179 | 0.89 |
| 630_L | 657_M | 1.179 | 0.89 |
| 73_G | 76_S | 1.178 | 0.89 |
| 51_L | 158_Y | 1.175 | 0.88 |
| 228_Y | 491_F | 1.174 | 0.88 |
| 353_R | 475_T | 1.168 | 0.88 |
| 558_L | 577_N | 1.164 | 0.88 |
| 41_E | 50_Y | 1.163 | 0.88 |
| 408_L | 428_I | 1.161 | 0.88 |
| 528_W | 543_W | 1.159 | 0.88 |
| 144_I | 160_N | 1.152 | 0.87 |
| 25_T | 30_F | 1.150 | 0.87 |
| 48_L | 55_G | 1.150 | 0.87 |
| 327_I | 330_K | 1.150 | 0.87 |
| 526_K | 530_D | 1.148 | 0.87 |
| 620_Y | 625_N | 1.146 | 0.87 |
| 148_L | 158_Y | 1.142 | 0.87 |
| 637_I | 650_A | 1.142 | 0.87 |
| 215_Y | 220_E | 1.141 | 0.86 |
| 165_H | 191_F | 1.138 | 0.86 |
| 385_M | 431_N | 1.137 | 0.86 |
| 523_R | 546_F | 1.136 | 0.86 |
| 429_Q | 558_L | 1.134 | 0.86 |
| 245_L | 265_H | 1.132 | 0.86 |
| 353_R | 526_K | 1.131 | 0.86 |
| 267_R | 271_N | 1.130 | 0.86 |
| 364_I | 394_L | 1.129 | 0.86 |
| 435_I | 439_K | 1.126 | 0.85 |
| 460_P | 475_T | 1.124 | 0.85 |
| 350_Y | 384_S | 1.120 | 0.85 |
| 236_P | 552_Y | 1.120 | 0.85 |
| 32_E | 35_E | 1.119 | 0.85 |
| 401_D | 432_V | 1.118 | 0.85 |
| 147_R | 546_F | 1.118 | 0.85 |
| 147_R | 157_T | 1.118 | 0.85 |
| 459_F | 474_D | 1.116 | 0.85 |
| 387_L | 432_V | 1.115 | 0.85 |
| 543_W | 560_G | 1.115 | 0.85 |
| 475_T | 490_G | 1.111 | 0.84 |
| 34_E | 38_A | 1.108 | 0.84 |
| 212_A | 246_L | 1.103 | 0.84 |
| 145_V | 149_E | 1.103 | 0.84 |
| 245_L | 249_Y | 1.103 | 0.84 |
| 493_K | 545_G | 1.099 | 0.84 |
| 524_Y | 560_G | 1.096 | 0.83 |
| 141_G | 145_V | 1.094 | 0.83 |
| 665_Q | 668_L | 1.092 | 0.83 |
| 367_R | 371_E | 1.090 | 0.83 |
| 595_P | 598_D | 1.088 | 0.83 |
| 212_A | 224_A | 1.088 | 0.83 |
| 429_Q | 523_R | 1.086 | 0.83 |
| 486_N | 628_E | 1.083 | 0.82 |
| 231_I | 373_A | 1.083 | 0.82 |
| 41_E | 54_Y | 1.078 | 0.82 |
| 520_R | 546_F | 1.078 | 0.82 |
| 38_A | 405_N | 1.077 | 0.82 |
| 39_R | 42_N | 1.077 | 0.82 |
| 350_Y | 429_Q | 1.077 | 0.82 |
| 367_R | 394_L | 1.076 | 0.82 |
| 189_I | 263_I | 1.072 | 0.81 |
| 390_N | 394_L | 1.070 | 0.81 |
| 68_F | 72_F | 1.069 | 0.81 |
| 24_E | 32_E | 1.069 | 0.81 |
| 55_G | 67_A | 1.069 | 0.81 |
| 436_Y | 458_E | 1.068 | 0.81 |
| 222_G | 364_I | 1.067 | 0.81 |
| 44_L | 47_H | 1.065 | 0.81 |
| 454_D | 486_N | 1.065 | 0.81 |
| 144_I | 543_W | 1.065 | 0.81 |
| 302_R | 323_I | 1.061 | 0.81 |
| 197_T | 375_T | 1.058 | 0.80 |
| 488_L | 526_K | 1.057 | 0.80 |
| 258_N | 396_N | 1.054 | 0.80 |
| 494_A | 497_V | 1.053 | 0.80 |
| 218_R | 360_I | 1.051 | 0.80 |
| 344_S | 466_P | 1.050 | 0.80 |
| 570_Q | 625_N | 1.048 | 0.79 |
| 577_N | 581_V | 1.046 | 0.79 |
| 211_I | 616_I | 1.044 | 0.79 |
| 354_G | 366_A | 1.044 | 0.79 |
| 365_Q | 538_A | 1.041 | 0.79 |
| 231_I | 494_A | 1.040 | 0.79 |
| 353_R | 357_F | 1.039 | 0.79 |
| 212_A | 227_F | 1.038 | 0.78 |
| 229_N | 233_E | 1.036 | 0.78 |
| 614_N | 653_N | 1.036 | 0.78 |
| 429_Q | 458_E | 1.033 | 0.78 |
| 192_Y | 210_G | 1.033 | 0.78 |
| 189_I | 215_Y | 1.032 | 0.78 |
| 302_R | 472_A | 1.032 | 0.78 |
| 528_W | 560_G | 1.031 | 0.78 |
| 618_A | 653_N | 1.031 | 0.78 |
| 162_G | 195_V | 1.031 | 0.78 |
| 68_F | 630_L | 1.030 | 0.78 |
| 405_N | 409_K | 1.030 | 0.78 |
| 229_N | 249_Y | 1.028 | 0.78 |
| 55_G | 74_K | 1.028 | 0.78 |
| 494_A | 636_A | 1.028 | 0.78 |
| 355_R | 386_E | 1.026 | 0.77 |
| 232_V | 241_G | 1.026 | 0.77 |
| 536_F | 564_A | 1.022 | 0.77 |
| 35_E | 39_R | 1.020 | 0.77 |
| 321_L | 488_L | 1.019 | 0.77 |
| 545_G | 580_K | 1.019 | 0.77 |
| 613_Y | 617_G | 1.013 | 0.76 |
| 357_F | 362_E | 1.013 | 0.76 |
| 152_T | 202_P | 1.011 | 0.76 |
| 485_K | 537_A | 1.011 | 0.76 |
| 522_L | 612_A | 1.007 | 0.75 |
| 39_R | 43_I | 1.004 | 0.75 |
| 372_K | 635_K | 1.003 | 0.75 |
| 386_E | 389_E | 1.002 | 0.75 |
| 671_D | 675_P | 1.001 | 0.75 |
| 233_E | 496_S | 1.001 | 0.75 |
| 631_K | 635_K | 1.000 | 0.75 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4bujB | 2 | 0.828 | 100 | 0.479 | Contact Map |
| 4kvmA | 4 | 0.809 | 100 | 0.514 | Contact Map |
| 4hnyA | 2 | 0.723 | 100 | 0.53 | Contact Map |
| 4ui9J | 1 | 0 | 100 | 0.534 | Contact Map |
| 4rg9A | 2 | 0.621 | 100 | 0.535 | Contact Map |
| 1w3bA | 2 | 0.5656 | 100 | 0.539 | Contact Map |
| 4ui9X | 2 | 0 | 100 | 0.542 | Contact Map |
| 4uzyA | 1 | 0.7784 | 100 | 0.543 | Contact Map |
| 2xpiA | 2 | 0.7041 | 100 | 0.55 | Contact Map |
| 4ui9C | 2 | 0 | 100 | 0.554 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)