| ATG16L2_v1 |
| ID: | 1470077002 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 513 (370) | ||
| Sequences: | 114962 (69938.5) | ||
| Seq/Len: | 310.708 | ||
| Nf(neff/√len): | 3635.9 |
Jackhmmer Results: (2016_04)
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: 310.708).
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 |
| 279_S | 292_A | 3.323 | 1.00 |
| 321_A | 334_G | 3.263 | 1.00 |
| 315_H | 333_T | 3.058 | 1.00 |
| 229_H | 247_T | 2.960 | 1.00 |
| 235_A | 248_G | 2.944 | 1.00 |
| 332_V | 342_E | 2.929 | 1.00 |
| 273_A | 291_A | 2.840 | 1.00 |
| 299_Q | 308_S | 2.787 | 1.00 |
| 290_L | 300_L | 2.685 | 1.00 |
| 254_I | 291_A | 2.611 | 1.00 |
| 281_D | 323_K | 2.597 | 1.00 |
| 371_I | 381_F | 2.569 | 1.00 |
| 246_A | 282_F | 2.549 | 1.00 |
| 290_L | 324_F | 2.523 | 1.00 |
| 412_L | 422_V | 2.479 | 1.00 |
| 291_A | 301_W | 2.437 | 1.00 |
| 298_A | 333_T | 2.397 | 1.00 |
| 320_T | 336_R | 2.358 | 1.00 |
| 401_S | 414_C | 2.336 | 1.00 |
| 362_D | 373_G | 2.334 | 1.00 |
| 299_Q | 311_T | 2.326 | 1.00 |
| 341_K | 350_C | 2.300 | 1.00 |
| 246_A | 289_V | 2.299 | 1.00 |
| 333_T | 343_W | 2.291 | 1.00 |
| 290_L | 331_A | 2.271 | 1.00 |
| 278_T | 294_Y | 2.258 | 1.00 |
| 237_R | 281_D | 2.243 | 1.00 |
| 459_A | 469_W | 2.238 | 1.00 |
| 413_S | 423_I | 2.216 | 1.00 |
| 247_T | 257_W | 2.186 | 1.00 |
| 372_S | 382_W | 2.171 | 1.00 |
| 283_D | 324_F | 2.140 | 1.00 |
| 246_A | 256_L | 2.074 | 1.00 |
| 371_I | 404_L | 2.042 | 1.00 |
| 484_H | 502_S | 2.029 | 1.00 |
| 341_K | 353_T | 2.028 | 1.00 |
| 234_N | 250_A | 1.922 | 1.00 |
| 395_V | 413_S | 1.888 | 1.00 |
| 447_K | 460_G | 1.857 | 1.00 |
| 248_G | 277_I | 1.852 | 1.00 |
| 325_K | 365_C | 1.836 | 1.00 |
| 255_H | 269_T | 1.827 | 1.00 |
| 332_V | 365_C | 1.817 | 1.00 |
| 290_L | 322_A | 1.809 | 1.00 |
| 246_A | 280_V | 1.786 | 1.00 |
| 490_A | 503_V | 1.769 | 1.00 |
| 302_K | 305_E | 1.757 | 1.00 |
| 258_N | 261_G | 1.756 | 1.00 |
| 458_L | 468_I | 1.749 | 1.00 |
| 323_K | 364_V | 1.687 | 1.00 |
| 412_L | 450_F | 1.666 | 1.00 |
| 424_D | 427_V | 1.654 | 1.00 |
| 361_N | 365_C | 1.652 | 1.00 |
| 350_C | 353_T | 1.652 | 1.00 |
| 266_A | 269_T | 1.630 | 1.00 |
| 458_L | 493_W | 1.611 | 1.00 |
| 340_V | 372_S | 1.611 | 1.00 |
| 239_G | 282_F | 1.607 | 1.00 |
| 344_D | 347_R | 1.604 | 1.00 |
| 383_D | 386_G | 1.597 | 1.00 |
| 334_G | 360_C | 1.574 | 1.00 |
| 281_D | 322_A | 1.564 | 1.00 |
| 239_G | 243_S | 1.553 | 1.00 |
| 308_S | 311_T | 1.541 | 1.00 |
| 332_V | 370_I | 1.515 | 1.00 |
| 315_H | 335_S | 1.505 | 1.00 |
| 273_A | 293_T | 1.502 | 1.00 |
| 291_A | 299_Q | 1.495 | 1.00 |
| 423_I | 430_I | 1.489 | 1.00 |
| 357_L | 372_S | 1.471 | 1.00 |
| 470_D | 473_T | 1.462 | 1.00 |
| 283_D | 287_Y | 1.462 | 1.00 |
| 248_G | 280_V | 1.461 | 1.00 |
| 292_A | 322_A | 1.459 | 1.00 |
| 255_H | 266_A | 1.444 | 1.00 |
| 382_W | 389_C | 1.442 | 1.00 |
| 325_K | 330_Q | 1.411 | 1.00 |
| 325_K | 329_H | 1.406 | 0.99 |
| 414_C | 445_W | 1.400 | 0.99 |
| 240_P | 286_G | 1.398 | 0.99 |
| 293_T | 297_A | 1.394 | 0.99 |
| 380_R | 389_C | 1.389 | 0.99 |
| 293_T | 296_Q | 1.376 | 0.99 |
| 292_A | 319_V | 1.375 | 0.99 |
| 247_T | 255_H | 1.353 | 0.99 |
| 237_R | 280_V | 1.343 | 0.99 |
| 279_S | 321_A | 1.340 | 0.99 |
| 380_R | 392_V | 1.334 | 0.99 |
| 238_F | 245_L | 1.329 | 0.99 |
| 281_D | 324_F | 1.329 | 0.99 |
| 469_W | 476_L | 1.323 | 0.99 |
| 282_F | 303_V | 1.318 | 0.99 |
| 283_D | 288_Q | 1.316 | 0.99 |
| 374_H | 380_R | 1.316 | 0.99 |
| 379_I | 413_S | 1.310 | 0.99 |
| 314_G | 343_W | 1.309 | 0.99 |
| 403_S | 449_V | 1.299 | 0.99 |
| 314_G | 341_K | 1.297 | 0.99 |
| 333_T | 341_K | 1.295 | 0.99 |
| 329_H | 346_G | 1.293 | 0.99 |
| 371_I | 411_L | 1.291 | 0.99 |
| 494_C | 497_G | 1.276 | 0.99 |
| 335_S | 339_T | 1.276 | 0.99 |
| 229_H | 249_G | 1.263 | 0.99 |
| 413_S | 421_K | 1.259 | 0.99 |
| 373_G | 399_V | 1.258 | 0.99 |
| 301_W | 308_S | 1.254 | 0.99 |
| 282_F | 289_V | 1.251 | 0.99 |
| 364_V | 403_S | 1.243 | 0.98 |
| 323_K | 363_V | 1.241 | 0.98 |
| 324_F | 331_A | 1.241 | 0.98 |
| 249_G | 252_R | 1.234 | 0.98 |
| 405_S | 450_F | 1.234 | 0.98 |
| 249_G | 253_L | 1.227 | 0.98 |
| 279_S | 322_A | 1.222 | 0.98 |
| 284_P | 324_F | 1.219 | 0.98 |
| 404_L | 411_L | 1.216 | 0.98 |
| 415_S | 421_K | 1.214 | 0.98 |
| 245_L | 259_V | 1.214 | 0.98 |
| 343_W | 350_C | 1.214 | 0.98 |
| 389_C | 392_V | 1.210 | 0.98 |
| 297_A | 311_T | 1.208 | 0.98 |
| 372_S | 380_R | 1.206 | 0.98 |
| 298_A | 322_A | 1.198 | 0.98 |
| 238_F | 259_V | 1.192 | 0.98 |
| 461_S | 467_Y | 1.190 | 0.98 |
| 322_A | 331_A | 1.187 | 0.98 |
| 405_S | 409_L | 1.187 | 0.98 |
| 324_F | 345_L | 1.187 | 0.98 |
| 374_H | 377_Q | 1.186 | 0.98 |
| 330_Q | 342_E | 1.184 | 0.98 |
| 222_A | 225_V | 1.184 | 0.98 |
| 466_L | 502_S | 1.173 | 0.98 |
| 339_T | 353_T | 1.173 | 0.98 |
| 325_K | 328_R | 1.168 | 0.97 |
| 315_H | 319_V | 1.166 | 0.97 |
| 356_V | 372_S | 1.166 | 0.97 |
| 278_T | 320_T | 1.165 | 0.97 |
| 318_K | 336_R | 1.161 | 0.97 |
| 369_I | 381_F | 1.159 | 0.97 |
| 276_S | 294_Y | 1.155 | 0.97 |
| 244_L | 256_L | 1.152 | 0.97 |
| 303_V | 306_A | 1.151 | 0.97 |
| 236_V | 247_T | 1.149 | 0.97 |
| 302_K | 309_K | 1.147 | 0.97 |
| 239_G | 244_L | 1.147 | 0.97 |
| 414_C | 448_A | 1.147 | 0.97 |
| 412_L | 457_A | 1.139 | 0.97 |
| 325_K | 332_V | 1.137 | 0.97 |
| 332_V | 363_V | 1.136 | 0.97 |
| 360_C | 365_C | 1.135 | 0.97 |
| 251_D | 255_H | 1.133 | 0.97 |
| 334_G | 363_V | 1.129 | 0.97 |
| 288_Q | 309_K | 1.129 | 0.97 |
| 412_L | 448_A | 1.127 | 0.97 |
| 240_P | 282_F | 1.120 | 0.96 |
| 243_S | 258_N | 1.117 | 0.96 |
| 406_H | 450_F | 1.116 | 0.96 |
| 275_G | 294_Y | 1.106 | 0.96 |
| 320_T | 334_G | 1.104 | 0.96 |
| 494_C | 498_S | 1.099 | 0.96 |
| 289_V | 303_V | 1.095 | 0.96 |
| 465_A | 479_R | 1.093 | 0.96 |
| 502_S | 512_W | 1.093 | 0.96 |
| 280_V | 291_A | 1.090 | 0.96 |
| 321_A | 362_D | 1.090 | 0.96 |
| 451_S | 455_S | 1.085 | 0.96 |
| 364_V | 402_L | 1.085 | 0.96 |
| 287_Y | 304_G | 1.084 | 0.96 |
| 368_H | 385_R | 1.079 | 0.95 |
| 288_Q | 300_L | 1.073 | 0.95 |
| 272_G | 301_W | 1.073 | 0.95 |
| 403_S | 448_A | 1.069 | 0.95 |
| 467_Y | 476_L | 1.065 | 0.95 |
| 268_Q | 306_A | 1.062 | 0.95 |
| 451_S | 456_Y | 1.059 | 0.95 |
| 302_K | 306_A | 1.059 | 0.95 |
| 484_H | 504_D | 1.058 | 0.95 |
| 335_S | 338_R | 1.057 | 0.95 |
| 409_L | 426_R | 1.057 | 0.95 |
| 405_S | 410_H | 1.056 | 0.95 |
| 402_L | 413_S | 1.055 | 0.95 |
| 273_A | 277_I | 1.054 | 0.95 |
| 410_H | 422_V | 1.053 | 0.95 |
| 287_Y | 302_K | 1.050 | 0.94 |
| 323_K | 332_V | 1.045 | 0.94 |
| 294_Y | 318_K | 1.044 | 0.94 |
| 254_I | 280_V | 1.043 | 0.94 |
| 400_T | 416_R | 1.040 | 0.94 |
| 395_V | 415_S | 1.035 | 0.94 |
| 322_A | 333_T | 1.035 | 0.94 |
| 315_H | 341_K | 1.035 | 0.94 |
| 330_Q | 351_S | 1.034 | 0.94 |
| 361_N | 375_N | 1.033 | 0.94 |
| 300_L | 312_L | 1.028 | 0.94 |
| 284_P | 328_R | 1.027 | 0.94 |
| 258_N | 267_N | 1.022 | 0.93 |
| 373_G | 402_L | 1.022 | 0.93 |
| 420_L | 459_A | 1.021 | 0.93 |
| 425_L | 428_S | 1.014 | 0.93 |
| 378_K | 392_V | 1.013 | 0.93 |
| 329_H | 344_D | 1.012 | 0.93 |
| 281_D | 290_L | 1.009 | 0.93 |
| 415_S | 419_T | 1.008 | 0.93 |
| 239_G | 242_S | 1.007 | 0.93 |
| 244_L | 267_N | 1.007 | 0.93 |
| 297_A | 313_S | 1.007 | 0.93 |
| 310_E | 348_A | 1.004 | 0.93 |
| 283_D | 290_L | 1.002 | 0.92 |
| 456_Y | 468_I | 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 | |
| 1vyhC | 10 | 0.5712 | 100 | 0.298 | Contact Map |
| 3j60g | 1 | 0.6764 | 100 | 0.323 | Contact Map |
| 1gotB | 1 | 0.6452 | 100 | 0.326 | Contact Map |
| 4wjuA | 2 | 0.6959 | 100 | 0.338 | Contact Map |
| 1erjA | 3 | 0.6472 | 100 | 0.339 | Contact Map |
| 3ow8A | 4 | 0.5653 | 100 | 0.34 | Contact Map |
| 4u1eI | 1 | 0.5517 | 100 | 0.343 | Contact Map |
| 4j87A | 1 | 0.5614 | 100 | 0.345 | Contact Map |
| 5a1uD | 1 | 0 | 100 | 0.35 | Contact Map |
| 2pbiB | 2 | 0.6667 | 100 | 0.352 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)