| uni_loca_hh |
| ID: | 1508164146 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 435 (410) | ||
| Sequences: | 6234 (4233.6) | ||
| Seq/Len: | 15.205 | ||
| Nf(neff/√len): | 209.1 |
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: 15.205).
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 |
| 214_G | 260_I | 4.188 | 1.00 |
| 252_K | 391_A | 4.122 | 1.00 |
| 350_C | 393_I | 3.632 | 1.00 |
| 332_A | 349_V | 3.335 | 1.00 |
| 354_M | 389_I | 3.225 | 1.00 |
| 296_T | 301_V | 3.168 | 1.00 |
| 49_G | 67_A | 3.123 | 1.00 |
| 171_F | 266_L | 3.002 | 1.00 |
| 401_S | 404_S | 2.958 | 1.00 |
| 129_R | 174_A | 2.817 | 1.00 |
| 207_W | 286_P | 2.791 | 1.00 |
| 67_A | 166_F | 2.745 | 1.00 |
| 86_T | 134_S | 2.732 | 1.00 |
| 213_L | 217_C | 2.659 | 1.00 |
| 69_C | 89_F | 2.644 | 1.00 |
| 131_T | 135_L | 2.639 | 1.00 |
| 227_D | 231_G | 2.520 | 1.00 |
| 78_A | 158_H | 2.495 | 1.00 |
| 182_S | 316_R | 2.454 | 1.00 |
| 45_L | 166_F | 2.440 | 1.00 |
| 249_G | 388_L | 2.374 | 1.00 |
| 314_L | 334_S | 2.348 | 1.00 |
| 314_L | 330_T | 2.324 | 1.00 |
| 203_W | 267_H | 2.281 | 1.00 |
| 73_L | 86_T | 2.278 | 1.00 |
| 294_E | 394_M | 2.268 | 1.00 |
| 208_R | 261_L | 2.261 | 1.00 |
| 207_W | 263_D | 2.253 | 1.00 |
| 267_H | 283_G | 2.211 | 1.00 |
| 297_H | 301_V | 2.152 | 1.00 |
| 248_A | 391_A | 2.150 | 1.00 |
| 392_Y | 409_C | 2.133 | 1.00 |
| 68_V | 162_A | 2.112 | 1.00 |
| 185_R | 312_R | 2.111 | 1.00 |
| 325_W | 329_Q | 2.110 | 1.00 |
| 346_F | 396_A | 2.031 | 1.00 |
| 70_A | 90_Q | 2.026 | 1.00 |
| 323_R | 326_P | 2.017 | 1.00 |
| 102_H | 106_Y | 1.983 | 1.00 |
| 76_S | 82_V | 1.965 | 1.00 |
| 285_V | 309_S | 1.952 | 1.00 |
| 350_C | 354_M | 1.946 | 1.00 |
| 297_H | 382_T | 1.929 | 1.00 |
| 308_Q | 312_R | 1.903 | 1.00 |
| 298_R | 358_D | 1.875 | 1.00 |
| 41_Y | 164_P | 1.872 | 1.00 |
| 23_A | 47_G | 1.867 | 1.00 |
| 200_H | 283_G | 1.859 | 1.00 |
| 161_K | 164_P | 1.859 | 1.00 |
| 66_P | 90_Q | 1.853 | 1.00 |
| 44_L | 167_S | 1.822 | 1.00 |
| 70_A | 130_V | 1.820 | 1.00 |
| 183_F | 187_Q | 1.812 | 1.00 |
| 328_L | 349_V | 1.808 | 1.00 |
| 396_A | 405_L | 1.798 | 1.00 |
| 130_V | 169_L | 1.778 | 1.00 |
| 70_A | 86_T | 1.776 | 1.00 |
| 200_H | 267_H | 1.769 | 1.00 |
| 286_P | 289_D | 1.762 | 1.00 |
| 26_F | 43_F | 1.754 | 1.00 |
| 351_W | 390_I | 1.746 | 1.00 |
| 383_W | 387_Q | 1.745 | 1.00 |
| 132_S | 168_Y | 1.738 | 1.00 |
| 346_F | 402_L | 1.709 | 1.00 |
| 61_V | 65_T | 1.707 | 1.00 |
| 71_V | 75_C | 1.703 | 1.00 |
| 300_S | 359_Y | 1.700 | 1.00 |
| 101_L | 105_E | 1.682 | 1.00 |
| 84_R | 88_C | 1.656 | 1.00 |
| 162_A | 166_F | 1.648 | 1.00 |
| 318_V | 333_F | 1.644 | 1.00 |
| 300_S | 358_D | 1.639 | 1.00 |
| 74_L | 137_I | 1.633 | 1.00 |
| 135_L | 139_E | 1.622 | 1.00 |
| 73_L | 82_V | 1.618 | 1.00 |
| 104_T | 108_L | 1.585 | 1.00 |
| 399_V | 405_L | 1.576 | 1.00 |
| 245_W | 412_Y | 1.575 | 1.00 |
| 49_G | 170_L | 1.574 | 1.00 |
| 164_P | 191_Q | 1.564 | 1.00 |
| 343_G | 399_V | 1.543 | 1.00 |
| 320_Q | 323_R | 1.536 | 1.00 |
| 331_F | 334_S | 1.532 | 1.00 |
| 328_L | 352_A | 1.531 | 1.00 |
| 396_A | 409_C | 1.531 | 1.00 |
| 72_A | 76_S | 1.529 | 1.00 |
| 396_A | 406_W | 1.526 | 1.00 |
| 106_Y | 342_P | 1.519 | 1.00 |
| 74_L | 77_L | 1.518 | 1.00 |
| 336_W | 345_V | 1.513 | 1.00 |
| 311_A | 315_R | 1.503 | 1.00 |
| 239_E | 243_V | 1.498 | 1.00 |
| 400_R | 404_S | 1.495 | 1.00 |
| 106_Y | 111_P | 1.488 | 1.00 |
| 69_C | 73_L | 1.488 | 1.00 |
| 50_A | 54_A | 1.463 | 1.00 |
| 299_I | 354_M | 1.450 | 1.00 |
| 129_R | 181_C | 1.425 | 1.00 |
| 406_W | 410_N | 1.422 | 1.00 |
| 384_A | 388_L | 1.404 | 0.99 |
| 77_L | 82_V | 1.401 | 0.99 |
| 105_E | 110_E | 1.383 | 0.99 |
| 204_A | 264_S | 1.361 | 0.99 |
| 208_R | 268_A | 1.355 | 0.99 |
| 186_F | 190_V | 1.336 | 0.99 |
| 224_R | 228_A | 1.327 | 0.99 |
| 244_V | 408_L | 1.327 | 0.99 |
| 320_Q | 324_A | 1.323 | 0.99 |
| 255_Y | 394_M | 1.314 | 0.99 |
| 390_I | 394_M | 1.308 | 0.99 |
| 83_H | 87_F | 1.306 | 0.99 |
| 322_S | 329_Q | 1.303 | 0.99 |
| 331_F | 355_V | 1.300 | 0.99 |
| 224_R | 227_D | 1.292 | 0.99 |
| 407_L | 411_S | 1.292 | 0.99 |
| 46_T | 50_A | 1.289 | 0.99 |
| 297_H | 383_W | 1.285 | 0.99 |
| 130_V | 165_Y | 1.274 | 0.99 |
| 141_K | 184_Q | 1.271 | 0.99 |
| 402_L | 406_W | 1.263 | 0.99 |
| 43_F | 47_G | 1.254 | 0.99 |
| 300_S | 304_R | 1.254 | 0.99 |
| 392_Y | 417_P | 1.251 | 0.99 |
| 289_D | 308_Q | 1.245 | 0.98 |
| 201_S | 268_A | 1.245 | 0.98 |
| 208_R | 265_L | 1.244 | 0.98 |
| 101_L | 104_T | 1.243 | 0.98 |
| 320_Q | 326_P | 1.241 | 0.98 |
| 74_L | 133_L | 1.236 | 0.98 |
| 88_C | 92_S | 1.234 | 0.98 |
| 319_F | 323_R | 1.228 | 0.98 |
| 174_A | 181_C | 1.223 | 0.98 |
| 53_V | 60_A | 1.223 | 0.98 |
| 334_S | 347_G | 1.218 | 0.98 |
| 91_M | 333_F | 1.218 | 0.98 |
| 30_C | 43_F | 1.210 | 0.98 |
| 189_R | 283_G | 1.202 | 0.98 |
| 332_A | 345_V | 1.201 | 0.98 |
| 41_Y | 163_L | 1.192 | 0.98 |
| 204_A | 268_A | 1.184 | 0.98 |
| 199_R | 203_W | 1.182 | 0.98 |
| 263_D | 286_P | 1.172 | 0.98 |
| 410_N | 414_S | 1.163 | 0.97 |
| 185_R | 285_V | 1.162 | 0.97 |
| 57_G | 61_V | 1.162 | 0.97 |
| 247_T | 408_L | 1.154 | 0.97 |
| 65_T | 89_F | 1.152 | 0.97 |
| 66_P | 127_T | 1.146 | 0.97 |
| 106_Y | 110_E | 1.145 | 0.97 |
| 163_L | 167_S | 1.144 | 0.97 |
| 159_V | 164_P | 1.143 | 0.97 |
| 395_L | 409_C | 1.143 | 0.97 |
| 87_F | 92_S | 1.135 | 0.97 |
| 66_P | 93_W | 1.132 | 0.97 |
| 242_Y | 246_T | 1.132 | 0.97 |
| 215_L | 258_H | 1.128 | 0.97 |
| 202_F | 206_S | 1.128 | 0.97 |
| 53_V | 57_G | 1.126 | 0.97 |
| 302_F | 394_M | 1.123 | 0.97 |
| 222_V | 227_D | 1.122 | 0.97 |
| 299_I | 386_T | 1.118 | 0.96 |
| 361_I | 365_A | 1.117 | 0.96 |
| 49_G | 64_F | 1.109 | 0.96 |
| 297_H | 379_R | 1.108 | 0.96 |
| 181_C | 285_V | 1.106 | 0.96 |
| 66_P | 130_V | 1.105 | 0.96 |
| 148_G | 152_R | 1.102 | 0.96 |
| 249_G | 391_A | 1.100 | 0.96 |
| 248_A | 395_L | 1.098 | 0.96 |
| 319_F | 326_P | 1.096 | 0.96 |
| 252_K | 387_Q | 1.085 | 0.96 |
| 387_Q | 391_A | 1.085 | 0.96 |
| 56_M | 60_A | 1.084 | 0.96 |
| 346_F | 349_V | 1.082 | 0.96 |
| 121_S | 124_M | 1.081 | 0.95 |
| 350_C | 389_I | 1.080 | 0.95 |
| 386_T | 390_I | 1.079 | 0.95 |
| 136_D | 317_L | 1.077 | 0.95 |
| 311_A | 327_L | 1.076 | 0.95 |
| 223_S | 227_D | 1.076 | 0.95 |
| 331_F | 352_A | 1.067 | 0.95 |
| 395_L | 405_L | 1.058 | 0.95 |
| 253_L | 257_S | 1.057 | 0.95 |
| 330_T | 334_S | 1.055 | 0.95 |
| 318_V | 334_S | 1.051 | 0.94 |
| 75_C | 160_C | 1.048 | 0.94 |
| 159_V | 191_Q | 1.047 | 0.94 |
| 252_K | 294_E | 1.045 | 0.94 |
| 395_L | 412_Y | 1.040 | 0.94 |
| 91_M | 318_V | 1.040 | 0.94 |
| 255_Y | 294_E | 1.039 | 0.94 |
| 328_L | 356_E | 1.037 | 0.94 |
| 91_M | 131_T | 1.032 | 0.94 |
| 354_M | 393_I | 1.031 | 0.94 |
| 100_G | 104_T | 1.020 | 0.93 |
| 299_I | 390_I | 1.017 | 0.93 |
| 212_I | 216_E | 1.017 | 0.93 |
| 388_L | 392_Y | 1.015 | 0.93 |
| 319_F | 324_A | 1.014 | 0.93 |
| 347_G | 394_M | 1.013 | 0.93 |
| 392_Y | 396_A | 1.012 | 0.93 |
| 407_L | 410_N | 1.012 | 0.93 |
| 390_I | 393_I | 1.012 | 0.93 |
| 309_S | 312_R | 1.006 | 0.93 |
| 299_I | 351_W | 1.004 | 0.93 |
| 139_E | 321_H | 1.003 | 0.93 |
| 331_F | 351_W | 1.000 | 0.92 |
| 302_F | 390_I | 1.000 | 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 | |
| 2wkbA | 6 | 0.0759 | 1.8 | 0.98 | Contact Map |
| 4cbfB | 3 | 0.0598 | 1.8 | 0.98 | Contact Map |
| 1wh5A | 1 | 0.0621 | 1.8 | 0.98 | Contact Map |
| 4cctD | 3 | 0.0598 | 1.8 | 0.98 | Contact Map |
| 1wh7A | 1 | 0.0621 | 1.7 | 0.98 | Contact Map |
| 3j27B | 3 | 0.0552 | 1.5 | 0.98 | Contact Map |
| 1rmkA | 1 | 0.0713 | 1.5 | 0.98 | Contact Map |
| 2losA | 1 | 0.2276 | 1.5 | 0.981 | Contact Map |
| 1xkmB | 2 | 0.0575 | 1.4 | 0.981 | Contact Map |
| 4ogqE | 1 | 0.0713 | 1.3 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)