| 20230302DL |
| ID: | 1677721558 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 487 (446) | ||
| Sequences: | 1401 (860.2) | ||
| Seq/Len: | 3.141 | ||
| Nf(neff/√len): | 40.7 |
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 |
| 377_V | 395_E | 4.446 | 1.00 |
| 211_G | 289_E | 3.954 | 1.00 |
| 298_L | 302_V | 3.906 | 1.00 |
| 294_P | 298_L | 3.291 | 1.00 |
| 178_R | 186_E | 2.959 | 1.00 |
| 160_A | 320_I | 2.671 | 1.00 |
| 371_D | 438_E | 2.596 | 1.00 |
| 167_A | 279_F | 2.584 | 1.00 |
| 284_Y | 306_K | 2.546 | 1.00 |
| 284_Y | 310_M | 2.532 | 1.00 |
| 170_R | 211_G | 2.477 | 1.00 |
| 377_V | 401_I | 2.468 | 1.00 |
| 379_I | 389_A | 2.457 | 1.00 |
| 374_L | 396_S | 2.355 | 1.00 |
| 155_F | 351_I | 2.215 | 1.00 |
| 167_A | 179_L | 2.160 | 1.00 |
| 8_E | 24_K | 2.066 | 1.00 |
| 155_F | 300_Y | 2.049 | 1.00 |
| 472_N | 476_D | 2.047 | 1.00 |
| 441_C | 456_L | 2.045 | 1.00 |
| 286_P | 289_E | 2.045 | 1.00 |
| 287_L | 306_K | 2.038 | 1.00 |
| 302_V | 305_S | 2.032 | 1.00 |
| 300_Y | 353_G | 1.989 | 1.00 |
| 332_K | 336_K | 1.970 | 1.00 |
| 37_L | 108_V | 1.948 | 1.00 |
| 380_Y | 391_G | 1.936 | 1.00 |
| 68_M | 96_D | 1.924 | 1.00 |
| 157_Q | 304_F | 1.909 | 0.99 |
| 64_T | 69_L | 1.880 | 0.99 |
| 94_I | 106_R | 1.877 | 0.99 |
| 294_P | 306_K | 1.846 | 0.99 |
| 156_A | 346_I | 1.828 | 0.99 |
| 2_I | 6_L | 1.807 | 0.99 |
| 323_Q | 334_I | 1.789 | 0.99 |
| 402_K | 477_V | 1.782 | 0.99 |
| 5_I | 25_N | 1.748 | 0.99 |
| 34_V | 66_T | 1.734 | 0.99 |
| 438_E | 463_R | 1.727 | 0.99 |
| 97_G | 105_L | 1.723 | 0.99 |
| 337_K | 341_Q | 1.707 | 0.99 |
| 225_K | 229_E | 1.690 | 0.98 |
| 158_L | 338_Y | 1.687 | 0.98 |
| 325_V | 330_E | 1.664 | 0.98 |
| 214_I | 281_V | 1.650 | 0.98 |
| 372_V | 477_V | 1.637 | 0.98 |
| 137_L | 215_D | 1.635 | 0.98 |
| 284_Y | 287_L | 1.628 | 0.98 |
| 165_C | 179_L | 1.623 | 0.98 |
| 304_F | 308_E | 1.589 | 0.97 |
| 164_R | 215_D | 1.558 | 0.97 |
| 321_E | 337_K | 1.557 | 0.97 |
| 330_E | 334_I | 1.555 | 0.97 |
| 281_V | 317_V | 1.552 | 0.97 |
| 158_L | 343_L | 1.532 | 0.97 |
| 376_I | 437_L | 1.516 | 0.96 |
| 167_A | 177_V | 1.514 | 0.96 |
| 9_I | 21_I | 1.490 | 0.96 |
| 153_P | 326_N | 1.486 | 0.96 |
| 181_S | 220_Y | 1.480 | 0.96 |
| 107_R | 113_L | 1.475 | 0.96 |
| 2_I | 34_V | 1.468 | 0.95 |
| 428_N | 434_G | 1.461 | 0.95 |
| 300_Y | 322_N | 1.455 | 0.95 |
| 17_Q | 20_A | 1.454 | 0.95 |
| 335_Y | 368_E | 1.449 | 0.95 |
| 323_Q | 330_E | 1.447 | 0.95 |
| 333_V | 337_K | 1.427 | 0.94 |
| 153_P | 324_V | 1.426 | 0.94 |
| 72_I | 92_G | 1.406 | 0.94 |
| 155_F | 322_N | 1.403 | 0.94 |
| 14_S | 17_Q | 1.402 | 0.94 |
| 457_F | 460_I | 1.401 | 0.94 |
| 31_L | 35_Y | 1.399 | 0.94 |
| 64_T | 97_G | 1.390 | 0.93 |
| 156_A | 348_L | 1.385 | 0.93 |
| 226_K | 229_E | 1.384 | 0.93 |
| 156_A | 325_V | 1.383 | 0.93 |
| 72_I | 89_E | 1.379 | 0.93 |
| 401_I | 451_T | 1.376 | 0.93 |
| 35_Y | 122_A | 1.376 | 0.93 |
| 98_K | 101_D | 1.373 | 0.93 |
| 210_E | 288_V | 1.360 | 0.92 |
| 195_E | 199_K | 1.358 | 0.92 |
| 327_N | 330_E | 1.357 | 0.92 |
| 167_A | 281_V | 1.355 | 0.92 |
| 75_T | 85_A | 1.354 | 0.92 |
| 163_A | 245_K | 1.351 | 0.92 |
| 201_T | 209_P | 1.349 | 0.92 |
| 216_G | 335_Y | 1.341 | 0.92 |
| 209_P | 287_L | 1.336 | 0.91 |
| 317_V | 437_L | 1.334 | 0.91 |
| 5_I | 21_I | 1.333 | 0.91 |
| 304_F | 322_N | 1.317 | 0.91 |
| 391_G | 406_G | 1.311 | 0.90 |
| 325_V | 331_A | 1.309 | 0.90 |
| 324_V | 327_N | 1.285 | 0.89 |
| 8_E | 21_I | 1.281 | 0.89 |
| 311_T | 317_V | 1.267 | 0.88 |
| 369_V | 442_N | 1.266 | 0.88 |
| 392_F | 409_L | 1.264 | 0.88 |
| 306_K | 309_Q | 1.255 | 0.88 |
| 353_G | 363_L | 1.254 | 0.87 |
| 8_E | 11_S | 1.248 | 0.87 |
| 77_A | 81_L | 1.240 | 0.87 |
| 301_D | 352_D | 1.237 | 0.87 |
| 156_A | 331_A | 1.227 | 0.86 |
| 216_G | 281_V | 1.216 | 0.85 |
| 5_I | 9_I | 1.214 | 0.85 |
| 85_A | 88_E | 1.199 | 0.84 |
| 16_K | 20_A | 1.194 | 0.84 |
| 148_K | 361_K | 1.193 | 0.84 |
| 3_L | 6_L | 1.188 | 0.83 |
| 409_L | 461_A | 1.171 | 0.82 |
| 5_I | 8_E | 1.169 | 0.82 |
| 330_E | 333_V | 1.167 | 0.82 |
| 282_W | 363_L | 1.166 | 0.82 |
| 305_S | 309_Q | 1.159 | 0.81 |
| 181_S | 368_E | 1.153 | 0.81 |
| 441_C | 444_W | 1.149 | 0.80 |
| 369_V | 441_C | 1.148 | 0.80 |
| 159_K | 217_E | 1.145 | 0.80 |
| 73_E | 109_M | 1.140 | 0.80 |
| 347_I | 364_Y | 1.140 | 0.80 |
| 281_V | 311_T | 1.138 | 0.80 |
| 72_I | 75_T | 1.125 | 0.78 |
| 392_F | 437_L | 1.125 | 0.78 |
| 242_S | 245_K | 1.123 | 0.78 |
| 16_K | 124_K | 1.120 | 0.78 |
| 181_S | 243_K | 1.120 | 0.78 |
| 335_Y | 339_I | 1.117 | 0.78 |
| 388_K | 418_H | 1.116 | 0.78 |
| 348_L | 366_F | 1.116 | 0.78 |
| 12_I | 17_Q | 1.114 | 0.78 |
| 169_V | 174_L | 1.110 | 0.77 |
| 187_Y | 190_L | 1.104 | 0.77 |
| 181_S | 358_A | 1.102 | 0.76 |
| 58_Q | 87_I | 1.101 | 0.76 |
| 385_D | 407_S | 1.101 | 0.76 |
| 139_S | 361_K | 1.100 | 0.76 |
| 385_D | 406_G | 1.100 | 0.76 |
| 415_V | 418_H | 1.094 | 0.76 |
| 64_T | 68_M | 1.091 | 0.75 |
| 399_G | 470_K | 1.091 | 0.75 |
| 160_A | 357_N | 1.091 | 0.75 |
| 103_E | 107_R | 1.088 | 0.75 |
| 70_D | 74_F | 1.087 | 0.75 |
| 335_Y | 369_V | 1.086 | 0.75 |
| 47_I | 317_V | 1.086 | 0.75 |
| 192_L | 195_E | 1.086 | 0.75 |
| 52_K | 56_A | 1.085 | 0.75 |
| 283_D | 303_R | 1.082 | 0.75 |
| 2_I | 5_I | 1.075 | 0.74 |
| 6_L | 108_V | 1.074 | 0.74 |
| 286_P | 295_A | 1.074 | 0.74 |
| 452_D | 474_F | 1.072 | 0.74 |
| 407_S | 459_P | 1.070 | 0.73 |
| 391_G | 405_A | 1.066 | 0.73 |
| 219_V | 223_Q | 1.065 | 0.73 |
| 156_A | 334_I | 1.064 | 0.73 |
| 45_Y | 278_K | 1.063 | 0.73 |
| 138_A | 141_Y | 1.060 | 0.72 |
| 163_A | 190_L | 1.059 | 0.72 |
| 296_F | 418_H | 1.059 | 0.72 |
| 350_N | 362_N | 1.058 | 0.72 |
| 226_K | 455_K | 1.053 | 0.72 |
| 136_M | 360_S | 1.052 | 0.72 |
| 247_F | 263_K | 1.046 | 0.71 |
| 12_I | 21_I | 1.037 | 0.70 |
| 155_F | 308_E | 1.037 | 0.70 |
| 159_K | 162_G | 1.035 | 0.70 |
| 193_L | 277_M | 1.035 | 0.70 |
| 405_A | 409_L | 1.034 | 0.70 |
| 323_Q | 337_K | 1.033 | 0.70 |
| 363_L | 468_K | 1.033 | 0.70 |
| 301_D | 351_I | 1.032 | 0.70 |
| 155_F | 304_F | 1.030 | 0.69 |
| 76_L | 89_E | 1.025 | 0.69 |
| 461_A | 464_L | 1.016 | 0.68 |
| 216_G | 279_F | 1.015 | 0.68 |
| 336_K | 340_D | 1.015 | 0.68 |
| 416_K | 419_E | 1.015 | 0.68 |
| 284_Y | 395_E | 1.010 | 0.67 |
| 447_S | 458_L | 1.004 | 0.66 |
| 300_Y | 304_F | 1.001 | 0.66 |
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 | |
| 3w1bA | 1 | 0.8994 | 100 | 0.281 | Contact Map |
| 2hivA | 1 | 0.8953 | 100 | 0.289 | Contact Map |
| 2cfmA | 1 | 0.9014 | 100 | 0.292 | Contact Map |
| 3gdeA | 1 | 0.8871 | 100 | 0.294 | Contact Map |
| 1x9nA | 1 | 0.8994 | 100 | 0.299 | Contact Map |
| 3l2pA | 1 | 0.8727 | 100 | 0.307 | Contact Map |
| 1vs0A | 2 | 0.5626 | 100 | 0.524 | Contact Map |
| 4d05A | 2 | 0.5236 | 100 | 0.555 | Contact Map |
| 1fviA | 1 | 0.5092 | 100 | 0.555 | Contact Map |
| 1a0iA | 1 | 0.6242 | 100 | 0.565 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)