| shortend1 |
| ID: | 1509124893 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 545 (511) | ||
| Sequences: | 10035 (7796.2) | ||
| Seq/Len: | 19.638 | ||
| Nf(neff/√len): | 344.9 |
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: 19.638).
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 |
| 228_A | 378_P | 3.637 | 1.00 |
| 259_A | 359_A | 3.048 | 1.00 |
| 24_R | 28_A | 2.806 | 1.00 |
| 25_L | 32_A | 2.759 | 1.00 |
| 100_A | 243_V | 2.698 | 1.00 |
| 180_H | 264_S | 2.660 | 1.00 |
| 220_D | 231_D | 2.637 | 1.00 |
| 1_E | 248_S | 2.636 | 1.00 |
| 179_L | 355_V | 2.632 | 1.00 |
| 156_S | 165_S | 2.609 | 1.00 |
| 246_R | 249_D | 2.602 | 1.00 |
| 245_K | 255_D | 2.556 | 1.00 |
| 226_F | 306_A | 2.551 | 1.00 |
| 17_D | 21_A | 2.545 | 1.00 |
| 225_S | 341_S | 2.542 | 1.00 |
| 22_L | 339_I | 2.541 | 1.00 |
| 96_T | 239_A | 2.533 | 1.00 |
| 366_T | 393_A | 2.512 | 1.00 |
| 284_E | 324_A | 2.508 | 1.00 |
| 258_L | 363_R | 2.507 | 1.00 |
| 367_V | 390_P | 2.469 | 1.00 |
| 228_A | 375_A | 2.466 | 1.00 |
| 463_D | 503_D | 2.458 | 1.00 |
| 2_P | 262_R | 2.453 | 1.00 |
| 115_Q | 192_D | 2.430 | 1.00 |
| 401_L | 419_E | 2.416 | 1.00 |
| 300_H | 401_L | 2.398 | 1.00 |
| 459_R | 503_D | 2.391 | 1.00 |
| 122_M | 151_A | 2.359 | 1.00 |
| 78_V | 86_M | 2.334 | 1.00 |
| 35_E | 61_R | 2.318 | 1.00 |
| 67_D | 70_R | 2.277 | 1.00 |
| 262_R | 419_E | 2.255 | 1.00 |
| 18_D | 21_A | 2.247 | 1.00 |
| 249_D | 252_A | 2.235 | 1.00 |
| 97_A | 195_L | 2.233 | 1.00 |
| 27_L | 366_T | 2.229 | 1.00 |
| 119_F | 185_S | 2.221 | 1.00 |
| 361_A | 368_P | 2.217 | 1.00 |
| 240_G | 352_L | 2.207 | 1.00 |
| 492_A | 498_L | 2.147 | 1.00 |
| 358_A | 402_A | 2.106 | 1.00 |
| 185_S | 191_C | 2.094 | 1.00 |
| 339_I | 353_A | 2.072 | 1.00 |
| 245_K | 253_A | 2.057 | 1.00 |
| 48_D | 53_A | 2.052 | 1.00 |
| 115_Q | 289_R | 2.036 | 1.00 |
| 366_T | 395_A | 2.031 | 1.00 |
| 388_E | 394_R | 1.991 | 1.00 |
| 184_Q | 188_A | 1.988 | 1.00 |
| 5_I | 355_V | 1.980 | 1.00 |
| 242_L | 355_V | 1.975 | 1.00 |
| 319_A | 336_V | 1.971 | 1.00 |
| 441_L | 498_L | 1.965 | 1.00 |
| 170_T | 173_S | 1.941 | 1.00 |
| 31_D | 222_R | 1.941 | 1.00 |
| 229_A | 374_E | 1.938 | 1.00 |
| 236_S | 346_T | 1.936 | 1.00 |
| 369_A | 393_A | 1.936 | 1.00 |
| 493_R | 497_A | 1.930 | 1.00 |
| 1_E | 4_A | 1.916 | 1.00 |
| 381_P | 384_A | 1.912 | 1.00 |
| 495_R | 499_L | 1.890 | 1.00 |
| 5_I | 359_A | 1.877 | 1.00 |
| 264_S | 416_V | 1.868 | 1.00 |
| 152_S | 167_T | 1.866 | 1.00 |
| 12_F | 353_A | 1.860 | 1.00 |
| 93_L | 120_V | 1.855 | 1.00 |
| 335_V | 388_E | 1.854 | 1.00 |
| 183_C | 261_V | 1.854 | 1.00 |
| 265_A | 290_A | 1.852 | 1.00 |
| 9_G | 96_T | 1.842 | 1.00 |
| 112_R | 160_G | 1.841 | 1.00 |
| 53_A | 56_K | 1.830 | 1.00 |
| 341_S | 371_L | 1.811 | 1.00 |
| 177_V | 414_A | 1.803 | 1.00 |
| 472_D | 475_C | 1.802 | 1.00 |
| 220_D | 224_K | 1.795 | 1.00 |
| 463_D | 499_L | 1.780 | 1.00 |
| 370_N | 373_A | 1.773 | 1.00 |
| 441_L | 492_A | 1.770 | 1.00 |
| 454_Q | 457_K | 1.766 | 1.00 |
| 42_D | 45_A | 1.758 | 1.00 |
| 335_V | 390_P | 1.726 | 1.00 |
| 227_S | 373_A | 1.721 | 1.00 |
| 103_Q | 258_L | 1.718 | 1.00 |
| 303_Y | 367_V | 1.703 | 1.00 |
| 341_S | 370_N | 1.697 | 1.00 |
| 454_Q | 458_L | 1.688 | 1.00 |
| 476_S | 480_T | 1.675 | 1.00 |
| 365_R | 400_R | 1.672 | 1.00 |
| 162_H | 285_A | 1.671 | 1.00 |
| 335_V | 394_R | 1.650 | 1.00 |
| 93_L | 155_L | 1.639 | 1.00 |
| 458_L | 477_L | 1.629 | 1.00 |
| 400_R | 420_R | 1.622 | 1.00 |
| 396_W | 400_R | 1.601 | 1.00 |
| 242_L | 352_L | 1.575 | 1.00 |
| 7_G | 103_Q | 1.563 | 1.00 |
| 240_G | 356_L | 1.563 | 1.00 |
| 16_A | 25_L | 1.561 | 1.00 |
| 153_G | 410_S | 1.561 | 1.00 |
| 21_A | 24_R | 1.560 | 1.00 |
| 398_D | 420_R | 1.560 | 1.00 |
| 442_V | 478_A | 1.555 | 1.00 |
| 177_V | 412_T | 1.554 | 1.00 |
| 227_S | 374_E | 1.544 | 1.00 |
| 488_A | 505_L | 1.540 | 1.00 |
| 343_L | 353_A | 1.537 | 1.00 |
| 20_E | 103_Q | 1.537 | 1.00 |
| 25_L | 30_T | 1.536 | 1.00 |
| 180_H | 190_E | 1.535 | 1.00 |
| 459_R | 499_L | 1.532 | 1.00 |
| 179_L | 416_V | 1.530 | 1.00 |
| 494_D | 497_A | 1.528 | 1.00 |
| 219_P | 231_D | 1.519 | 1.00 |
| 150_V | 275_L | 1.517 | 1.00 |
| 459_R | 463_D | 1.517 | 1.00 |
| 218_A | 224_K | 1.517 | 1.00 |
| 12_F | 240_G | 1.512 | 1.00 |
| 109_E | 482_T | 1.510 | 1.00 |
| 355_V | 418_L | 1.508 | 1.00 |
| 304_V | 322_L | 1.505 | 1.00 |
| 33_T | 63_G | 1.501 | 1.00 |
| 472_D | 476_S | 1.499 | 1.00 |
| 461_H | 465_H | 1.497 | 1.00 |
| 184_Q | 293_L | 1.496 | 1.00 |
| 97_A | 241_V | 1.494 | 1.00 |
| 358_A | 362_L | 1.492 | 1.00 |
| 179_L | 196_V | 1.490 | 1.00 |
| 27_L | 393_A | 1.489 | 1.00 |
| 179_L | 244_V | 1.485 | 1.00 |
| 10_C | 19_P | 1.484 | 1.00 |
| 446_R | 484_F | 1.475 | 1.00 |
| 31_D | 372_H | 1.466 | 1.00 |
| 445_G | 451_L | 1.463 | 1.00 |
| 297_E | 300_H | 1.460 | 1.00 |
| 251_L | 421_A | 1.460 | 1.00 |
| 34_R | 66_E | 1.459 | 1.00 |
| 286_V | 290_A | 1.455 | 1.00 |
| 120_V | 197_G | 1.443 | 1.00 |
| 373_A | 389_L | 1.442 | 1.00 |
| 195_L | 243_V | 1.441 | 1.00 |
| 303_Y | 358_A | 1.429 | 1.00 |
| 365_R | 420_R | 1.420 | 1.00 |
| 93_L | 241_V | 1.415 | 1.00 |
| 258_L | 359_A | 1.411 | 1.00 |
| 224_K | 229_A | 1.411 | 1.00 |
| 185_S | 190_E | 1.410 | 1.00 |
| 186_L | 246_R | 1.405 | 0.99 |
| 469_A | 472_D | 1.398 | 0.99 |
| 96_T | 241_V | 1.376 | 0.99 |
| 448_G | 486_R | 1.375 | 0.99 |
| 443_L | 455_A | 1.373 | 0.99 |
| 93_L | 151_A | 1.372 | 0.99 |
| 335_V | 367_V | 1.370 | 0.99 |
| 26_L | 360_L | 1.370 | 0.99 |
| 166_I | 181_L | 1.369 | 0.99 |
| 101_L | 243_V | 1.366 | 0.99 |
| 97_A | 155_L | 1.363 | 0.99 |
| 284_E | 288_R | 1.358 | 0.99 |
| 103_Q | 256_S | 1.357 | 0.99 |
| 267_N | 413_N | 1.354 | 0.99 |
| 475_C | 479_G | 1.351 | 0.99 |
| 117_G | 164_P | 1.350 | 0.99 |
| 24_R | 27_L | 1.347 | 0.99 |
| 382_W | 389_L | 1.335 | 0.99 |
| 447_T | 486_R | 1.329 | 0.99 |
| 365_R | 398_D | 1.329 | 0.99 |
| 8_A | 356_L | 1.328 | 0.99 |
| 3_I | 244_V | 1.323 | 0.99 |
| 403_G | 415_H | 1.323 | 0.99 |
| 3_I | 183_C | 1.317 | 0.99 |
| 101_L | 159_L | 1.314 | 0.99 |
| 362_L | 418_L | 1.310 | 0.99 |
| 168_I | 181_L | 1.308 | 0.99 |
| 16_A | 21_A | 1.306 | 0.99 |
| 330_R | 333_P | 1.305 | 0.99 |
| 8_A | 19_P | 1.304 | 0.99 |
| 197_G | 241_V | 1.299 | 0.99 |
| 247_L | 260_V | 1.296 | 0.99 |
| 224_K | 231_D | 1.291 | 0.99 |
| 289_R | 293_L | 1.290 | 0.99 |
| 326_Y | 403_G | 1.284 | 0.99 |
| 121_G | 174_S | 1.281 | 0.99 |
| 265_A | 286_V | 1.280 | 0.99 |
| 39_D | 69_D | 1.275 | 0.99 |
| 177_V | 266_V | 1.271 | 0.99 |
| 323_G | 385_L | 1.269 | 0.99 |
| 17_D | 66_E | 1.269 | 0.99 |
| 117_G | 191_C | 1.268 | 0.99 |
| 33_T | 61_R | 1.266 | 0.99 |
| 35_E | 60_R | 1.255 | 0.99 |
| 58_T | 212_S | 1.248 | 0.99 |
| 184_Q | 187_R | 1.245 | 0.98 |
| 98_W | 102_E | 1.241 | 0.98 |
| 447_T | 450_A | 1.241 | 0.98 |
| 107_V | 110_R | 1.240 | 0.98 |
| 193_T | 243_V | 1.234 | 0.98 |
| 377_H | 380_I | 1.233 | 0.98 |
| 312_R | 379_D | 1.226 | 0.98 |
| 63_G | 236_S | 1.221 | 0.98 |
| 490_V | 501_A | 1.217 | 0.98 |
| 179_L | 261_V | 1.214 | 0.98 |
| 198_S | 352_L | 1.212 | 0.98 |
| 238_G | 346_T | 1.208 | 0.98 |
| 360_L | 364_H | 1.205 | 0.98 |
| 446_R | 485_A | 1.201 | 0.98 |
| 441_L | 470_L | 1.198 | 0.98 |
| 474_A | 477_L | 1.195 | 0.98 |
| 296_V | 300_H | 1.194 | 0.98 |
| 256_S | 363_R | 1.189 | 0.98 |
| 96_T | 99_E | 1.176 | 0.98 |
| 227_S | 375_A | 1.175 | 0.98 |
| 75_F | 98_W | 1.172 | 0.98 |
| 455_A | 488_A | 1.153 | 0.97 |
| 273_A | 277_A | 1.149 | 0.97 |
| 180_H | 184_Q | 1.148 | 0.97 |
| 37_P | 40_R | 1.147 | 0.97 |
| 97_A | 159_L | 1.146 | 0.97 |
| 107_V | 482_T | 1.144 | 0.97 |
| 453_A | 457_K | 1.143 | 0.97 |
| 92_L | 239_A | 1.143 | 0.97 |
| 192_D | 249_D | 1.143 | 0.97 |
| 192_D | 246_R | 1.142 | 0.97 |
| 24_R | 30_T | 1.137 | 0.97 |
| 390_P | 394_R | 1.130 | 0.97 |
| 376_P | 382_W | 1.129 | 0.97 |
| 125_S | 148_G | 1.125 | 0.97 |
| 497_A | 501_A | 1.125 | 0.97 |
| 373_A | 376_P | 1.121 | 0.97 |
| 319_A | 380_I | 1.121 | 0.97 |
| 191_C | 194_A | 1.121 | 0.97 |
| 440_P | 489_A | 1.118 | 0.96 |
| 468_L | 473_L | 1.115 | 0.96 |
| 14_G | 32_A | 1.114 | 0.96 |
| 23_W | 368_P | 1.114 | 0.96 |
| 376_P | 389_L | 1.107 | 0.96 |
| 100_A | 195_L | 1.106 | 0.96 |
| 100_A | 241_V | 1.104 | 0.96 |
| 235_W | 347_Q | 1.103 | 0.96 |
| 443_L | 458_L | 1.099 | 0.96 |
| 296_V | 401_L | 1.098 | 0.96 |
| 153_G | 165_S | 1.095 | 0.96 |
| 441_L | 477_L | 1.094 | 0.96 |
| 182_A | 194_A | 1.092 | 0.96 |
| 195_L | 241_V | 1.091 | 0.96 |
| 499_L | 503_D | 1.076 | 0.95 |
| 120_V | 241_V | 1.075 | 0.95 |
| 266_V | 414_A | 1.075 | 0.95 |
| 12_F | 356_L | 1.073 | 0.95 |
| 439_L | 442_V | 1.071 | 0.95 |
| 456_A | 460_A | 1.069 | 0.95 |
| 503_D | 507_Q | 1.064 | 0.95 |
| 9_G | 100_A | 1.063 | 0.95 |
| 101_L | 111_L | 1.062 | 0.95 |
| 263_A | 293_L | 1.060 | 0.95 |
| 116_T | 193_T | 1.059 | 0.95 |
| 11_R | 99_E | 1.053 | 0.95 |
| 459_R | 506_A | 1.044 | 0.94 |
| 453_A | 456_A | 1.044 | 0.94 |
| 29_G | 369_A | 1.041 | 0.94 |
| 22_L | 343_L | 1.033 | 0.94 |
| 461_H | 468_L | 1.029 | 0.94 |
| 75_F | 484_F | 1.027 | 0.94 |
| 119_F | 191_C | 1.024 | 0.93 |
| 123_M | 348_A | 1.013 | 0.93 |
| 277_A | 313_L | 1.009 | 0.93 |
| 358_A | 404_V | 1.007 | 0.93 |
| 439_L | 471_A | 1.006 | 0.93 |
| 455_A | 505_L | 1.004 | 0.93 |
| 93_L | 197_G | 1.003 | 0.93 |
| 36_V | 208_F | 1.003 | 0.93 |
| 291_L | 326_Y | 1.002 | 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 | |
| 4na1A | 2 | 0.9761 | 100 | 0.139 | Contact Map |
| 2vz8A | 2 | 0.9486 | 100 | 0.139 | Contact Map |
| 4tktA | 1 | 0.9505 | 100 | 0.163 | Contact Map |
| 4zdnA | 1 | 0 | 100 | 0.171 | Contact Map |
| 4kc5A | 4 | 0.9872 | 100 | 0.176 | Contact Map |
| 4qyrA | 1 | 0.9596 | 100 | 0.181 | Contact Map |
| 4opeA | 4 | 0.9761 | 100 | 0.183 | Contact Map |
| 4mz0A | 2 | 0.9761 | 100 | 0.185 | Contact Map |
| 2qo3A | 2 | 0.9798 | 100 | 0.191 | Contact Map |
| 2hg4A | 6 | 0.9541 | 100 | 0.195 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)