| Yojk |
| ID: | 1698754878 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 414 (398) | ||
| Sequences: | 9590 (6114.8) | ||
| Seq/Len: | 24.095 | ||
| Nf(neff/√len): | 306.5 |
HHblits Results: (2016_02)
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 |
| 321_V | 362_V | 4.683 | 1.00 |
| 336_V | 342_G | 4.625 | 1.00 |
| 371_K | 374_E | 4.498 | 1.00 |
| 3_N | 31_N | 4.367 | 1.00 |
| 6_M | 22_M | 4.057 | 1.00 |
| 305_G | 322_V | 3.571 | 1.00 |
| 300_L | 362_V | 3.092 | 1.00 |
| 303_T | 320_L | 3.041 | 1.00 |
| 3_N | 33_T | 2.727 | 1.00 |
| 30_E | 393_L | 2.720 | 1.00 |
| 193_S | 379_L | 2.718 | 1.00 |
| 31_N | 50_E | 2.667 | 1.00 |
| 28_R | 390_D | 2.542 | 1.00 |
| 195_G | 378_S | 2.518 | 1.00 |
| 22_M | 49_I | 2.478 | 1.00 |
| 6_M | 105_I | 2.473 | 1.00 |
| 383_G | 386_K | 2.432 | 1.00 |
| 106_Y | 124_R | 2.372 | 1.00 |
| 301_F | 309_S | 2.359 | 1.00 |
| 41_K | 45_T | 2.355 | 1.00 |
| 4_V | 103_Y | 2.351 | 1.00 |
| 264_V | 294_I | 2.299 | 1.00 |
| 356_K | 360_Q | 2.292 | 1.00 |
| 343_K | 361_E | 2.250 | 1.00 |
| 376_G | 380_K | 2.245 | 1.00 |
| 5_L | 35_Y | 2.216 | 1.00 |
| 234_L | 300_L | 2.205 | 1.00 |
| 24_E | 27_S | 2.189 | 1.00 |
| 313_G | 320_L | 2.188 | 1.00 |
| 258_D | 356_K | 2.180 | 1.00 |
| 341_A | 375_I | 2.128 | 1.00 |
| 28_R | 389_A | 2.121 | 1.00 |
| 13_G | 17_P | 2.120 | 1.00 |
| 373_K | 376_G | 2.107 | 1.00 |
| 310_T | 336_V | 2.087 | 1.00 |
| 300_L | 359_I | 2.060 | 1.00 |
| 370_E | 374_E | 2.036 | 1.00 |
| 14_H | 107_D | 2.032 | 1.00 |
| 125_F | 187_L | 2.022 | 1.00 |
| 254_E | 352_E | 2.019 | 1.00 |
| 33_T | 52_R | 2.010 | 1.00 |
| 2_A | 30_E | 2.007 | 1.00 |
| 24_E | 28_R | 2.004 | 1.00 |
| 335_Q | 338_K | 2.003 | 1.00 |
| 28_R | 393_L | 1.999 | 1.00 |
| 369_A | 373_K | 1.996 | 1.00 |
| 314_L | 341_A | 1.982 | 1.00 |
| 125_F | 392_I | 1.978 | 1.00 |
| 24_E | 385_S | 1.972 | 1.00 |
| 235_F | 298_A | 1.962 | 1.00 |
| 93_Y | 119_M | 1.911 | 1.00 |
| 255_V | 359_I | 1.902 | 1.00 |
| 321_V | 358_T | 1.879 | 1.00 |
| 322_V | 333_A | 1.871 | 1.00 |
| 301_F | 313_G | 1.868 | 1.00 |
| 106_Y | 113_G | 1.863 | 1.00 |
| 387_K | 390_D | 1.862 | 1.00 |
| 360_Q | 364_N | 1.837 | 1.00 |
| 340_G | 371_K | 1.828 | 1.00 |
| 236_I | 256_C | 1.823 | 1.00 |
| 352_E | 356_K | 1.810 | 1.00 |
| 117_A | 124_R | 1.808 | 1.00 |
| 257_K | 282_N | 1.742 | 1.00 |
| 256_C | 263_V | 1.716 | 1.00 |
| 24_E | 386_K | 1.708 | 1.00 |
| 343_K | 362_V | 1.706 | 1.00 |
| 250_N | 254_E | 1.693 | 1.00 |
| 385_S | 389_A | 1.688 | 1.00 |
| 384_G | 388_A | 1.688 | 1.00 |
| 361_E | 365_N | 1.687 | 1.00 |
| 334_D | 338_K | 1.677 | 1.00 |
| 259_F | 360_Q | 1.671 | 1.00 |
| 234_L | 302_V | 1.643 | 1.00 |
| 317_E | 372_A | 1.625 | 1.00 |
| 302_V | 321_V | 1.624 | 1.00 |
| 235_F | 291_Q | 1.602 | 1.00 |
| 253_L | 283_F | 1.594 | 1.00 |
| 6_M | 18_S | 1.579 | 1.00 |
| 33_T | 99_E | 1.577 | 1.00 |
| 335_Q | 339_V | 1.573 | 1.00 |
| 231_E | 262_K | 1.564 | 1.00 |
| 357_E | 361_E | 1.557 | 1.00 |
| 391_S | 394_E | 1.557 | 1.00 |
| 314_L | 375_I | 1.552 | 1.00 |
| 4_V | 25_L | 1.548 | 1.00 |
| 18_S | 34_Y | 1.536 | 1.00 |
| 343_K | 358_T | 1.531 | 1.00 |
| 251_Q | 352_E | 1.518 | 1.00 |
| 255_V | 355_L | 1.510 | 1.00 |
| 370_E | 373_K | 1.510 | 1.00 |
| 301_F | 318_T | 1.504 | 1.00 |
| 314_L | 372_A | 1.503 | 1.00 |
| 361_E | 368_Y | 1.502 | 1.00 |
| 377_Q | 380_K | 1.467 | 1.00 |
| 377_Q | 381_A | 1.465 | 1.00 |
| 387_K | 391_S | 1.462 | 1.00 |
| 8_G | 18_S | 1.443 | 1.00 |
| 374_E | 377_Q | 1.437 | 1.00 |
| 362_V | 368_Y | 1.436 | 1.00 |
| 12_E | 16_N | 1.436 | 1.00 |
| 52_R | 95_E | 1.423 | 1.00 |
| 343_K | 368_Y | 1.416 | 1.00 |
| 321_V | 343_K | 1.416 | 1.00 |
| 286_R | 289_V | 1.409 | 1.00 |
| 374_E | 378_S | 1.403 | 0.99 |
| 33_T | 50_E | 1.403 | 0.99 |
| 373_K | 377_Q | 1.400 | 0.99 |
| 232_N | 299_S | 1.399 | 0.99 |
| 208_V | 391_S | 1.396 | 0.99 |
| 35_Y | 92_I | 1.387 | 0.99 |
| 386_K | 390_D | 1.386 | 0.99 |
| 235_F | 266_S | 1.372 | 0.99 |
| 228_I | 262_K | 1.362 | 0.99 |
| 104_V | 117_A | 1.359 | 0.99 |
| 4_V | 30_E | 1.358 | 0.99 |
| 36_A | 51_F | 1.355 | 0.99 |
| 308_N | 312_E | 1.348 | 0.99 |
| 322_V | 336_V | 1.342 | 0.99 |
| 118_N | 184_D | 1.336 | 0.99 |
| 94_E | 98_H | 1.315 | 0.99 |
| 5_L | 96_V | 1.308 | 0.99 |
| 93_Y | 120_L | 1.303 | 0.99 |
| 26_K | 49_I | 1.298 | 0.99 |
| 320_L | 336_V | 1.294 | 0.99 |
| 306_G | 309_S | 1.291 | 0.99 |
| 10_P | 14_H | 1.285 | 0.99 |
| 296_K | 316_F | 1.283 | 0.99 |
| 337_E | 344_V | 1.282 | 0.99 |
| 253_L | 265_L | 1.260 | 0.99 |
| 24_E | 389_A | 1.258 | 0.99 |
| 258_D | 353_S | 1.256 | 0.99 |
| 280_P | 283_F | 1.252 | 0.99 |
| 91_H | 94_E | 1.231 | 0.98 |
| 333_A | 344_V | 1.231 | 0.98 |
| 261_G | 360_Q | 1.231 | 0.98 |
| 26_K | 32_I | 1.229 | 0.98 |
| 365_N | 368_Y | 1.229 | 0.98 |
| 192_T | 197_Q | 1.228 | 0.98 |
| 6_M | 25_L | 1.220 | 0.98 |
| 368_Y | 371_K | 1.218 | 0.98 |
| 3_N | 102_D | 1.218 | 0.98 |
| 291_Q | 312_E | 1.198 | 0.98 |
| 5_L | 101_Y | 1.191 | 0.98 |
| 38_K | 53_E | 1.187 | 0.98 |
| 322_V | 342_G | 1.183 | 0.98 |
| 389_A | 393_L | 1.178 | 0.98 |
| 13_G | 16_N | 1.178 | 0.98 |
| 324_P | 329_Q | 1.176 | 0.98 |
| 22_M | 32_I | 1.174 | 0.98 |
| 354_L | 358_T | 1.173 | 0.98 |
| 368_Y | 372_A | 1.172 | 0.98 |
| 4_V | 32_I | 1.158 | 0.97 |
| 351_S | 354_L | 1.153 | 0.97 |
| 222_D | 225_F | 1.153 | 0.97 |
| 2_A | 102_D | 1.151 | 0.97 |
| 350_L | 355_L | 1.148 | 0.97 |
| 11_G | 107_D | 1.139 | 0.97 |
| 32_I | 49_I | 1.130 | 0.97 |
| 120_L | 123_P | 1.126 | 0.97 |
| 304_H | 309_S | 1.115 | 0.96 |
| 11_G | 241_I | 1.107 | 0.96 |
| 303_T | 322_V | 1.101 | 0.96 |
| 94_E | 97_K | 1.091 | 0.96 |
| 2_A | 396_V | 1.090 | 0.96 |
| 187_L | 208_V | 1.086 | 0.96 |
| 127_L | 213_S | 1.083 | 0.96 |
| 11_G | 14_H | 1.082 | 0.96 |
| 44_I | 51_F | 1.078 | 0.95 |
| 196_F | 339_V | 1.075 | 0.95 |
| 255_V | 356_K | 1.072 | 0.95 |
| 279_I | 285_V | 1.071 | 0.95 |
| 7_I | 113_G | 1.069 | 0.95 |
| 235_F | 295_L | 1.069 | 0.95 |
| 310_T | 320_L | 1.069 | 0.95 |
| 324_P | 333_A | 1.062 | 0.95 |
| 254_E | 257_K | 1.059 | 0.95 |
| 236_I | 263_V | 1.058 | 0.95 |
| 21_V | 213_S | 1.058 | 0.95 |
| 295_L | 301_F | 1.054 | 0.95 |
| 103_Y | 396_V | 1.048 | 0.94 |
| 303_T | 310_T | 1.047 | 0.94 |
| 113_G | 124_R | 1.046 | 0.94 |
| 341_A | 372_A | 1.040 | 0.94 |
| 366_R | 370_E | 1.035 | 0.94 |
| 340_G | 367_S | 1.034 | 0.94 |
| 341_A | 371_K | 1.034 | 0.94 |
| 372_A | 376_G | 1.033 | 0.94 |
| 258_D | 352_E | 1.033 | 0.94 |
| 291_Q | 295_L | 1.024 | 0.93 |
| 42_E | 46_A | 1.023 | 0.93 |
| 233_V | 298_A | 1.023 | 0.93 |
| 13_G | 308_N | 1.018 | 0.93 |
| 329_Q | 332_V | 1.013 | 0.93 |
| 292_L | 312_E | 1.013 | 0.93 |
| 239_G | 306_G | 1.009 | 0.93 |
| 118_N | 186_D | 1.003 | 0.93 |
| 304_H | 308_N | 1.001 | 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 | |
| 2iyaA | 2 | 0.9251 | 100 | 0.288 | Contact Map |
| 3rscA | 2 | 0.942 | 100 | 0.301 | Contact Map |
| 2iyfA | 2 | 0.9348 | 100 | 0.313 | Contact Map |
| 3ia7A | 2 | 0.9396 | 100 | 0.322 | Contact Map |
| 2pq6A | 1 | 0.9179 | 100 | 0.324 | Contact Map |
| 1rrvA | 2 | 0.9179 | 100 | 0.325 | Contact Map |
| 2p6pA | 2 | 0.8889 | 100 | 0.335 | Contact Map |
| 2vchA | 1 | 0.9348 | 100 | 0.338 | Contact Map |
| 3otiA | 2 | 0.8671 | 100 | 0.345 | Contact Map |
| 2yjnA | 1 | 0.9155 | 100 | 0.346 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)