| CSDHH |
| ID: | 1509410117 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 435 (412) | ||
| Sequences: | 3648 (2537.3) | ||
| Seq/Len: | 8.854 | ||
| Nf(neff/√len): | 125.0 |
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: 8.854).
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 |
| 252_K | 391_A | 4.105 | 1.00 |
| 296_T | 301_V | 3.745 | 1.00 |
| 219_N | 263_D | 3.672 | 1.00 |
| 219_N | 260_I | 3.578 | 1.00 |
| 354_M | 393_I | 3.560 | 1.00 |
| 212_I | 286_P | 3.306 | 1.00 |
| 358_D | 389_I | 3.298 | 1.00 |
| 86_T | 134_S | 3.030 | 1.00 |
| 401_S | 404_S | 2.988 | 1.00 |
| 171_F | 269_A | 2.963 | 1.00 |
| 129_R | 174_A | 2.940 | 1.00 |
| 332_A | 353_V | 2.936 | 1.00 |
| 49_G | 67_A | 2.914 | 1.00 |
| 131_T | 135_L | 2.803 | 1.00 |
| 260_I | 263_D | 2.690 | 1.00 |
| 182_S | 316_R | 2.668 | 1.00 |
| 341_H | 347_G | 2.653 | 1.00 |
| 69_C | 89_F | 2.631 | 1.00 |
| 23_A | 47_G | 2.623 | 1.00 |
| 78_A | 158_H | 2.574 | 1.00 |
| 26_F | 43_F | 2.557 | 1.00 |
| 110_E | 346_F | 2.549 | 1.00 |
| 67_A | 166_F | 2.509 | 1.00 |
| 294_E | 394_M | 2.481 | 1.00 |
| 297_H | 301_V | 2.407 | 1.00 |
| 314_L | 334_S | 2.358 | 1.00 |
| 70_A | 90_Q | 2.339 | 1.00 |
| 208_R | 270_G | 2.291 | 1.00 |
| 45_L | 166_F | 2.286 | 1.00 |
| 73_L | 86_T | 2.210 | 1.00 |
| 218_L | 221_A | 2.193 | 1.00 |
| 270_G | 283_G | 2.191 | 1.00 |
| 314_L | 330_T | 2.171 | 1.00 |
| 66_P | 90_Q | 2.170 | 1.00 |
| 44_L | 167_S | 2.168 | 1.00 |
| 212_I | 266_L | 2.155 | 1.00 |
| 325_W | 329_Q | 2.153 | 1.00 |
| 392_Y | 409_C | 2.137 | 1.00 |
| 79_P | 140_G | 2.106 | 1.00 |
| 248_A | 391_A | 2.098 | 1.00 |
| 285_V | 309_S | 2.095 | 1.00 |
| 213_L | 264_S | 2.059 | 1.00 |
| 201_S | 283_G | 1.989 | 1.00 |
| 308_Q | 312_R | 1.961 | 1.00 |
| 300_S | 363_S | 1.961 | 1.00 |
| 354_M | 358_D | 1.909 | 1.00 |
| 249_G | 388_L | 1.909 | 1.00 |
| 41_Y | 164_P | 1.902 | 1.00 |
| 350_C | 396_A | 1.896 | 1.00 |
| 68_V | 162_A | 1.894 | 1.00 |
| 328_L | 353_V | 1.888 | 1.00 |
| 132_S | 168_Y | 1.887 | 1.00 |
| 323_R | 326_P | 1.882 | 1.00 |
| 399_V | 405_L | 1.858 | 1.00 |
| 383_W | 387_Q | 1.846 | 1.00 |
| 70_A | 130_V | 1.839 | 1.00 |
| 76_S | 82_V | 1.822 | 1.00 |
| 298_R | 362_H | 1.820 | 1.00 |
| 130_V | 169_L | 1.814 | 1.00 |
| 297_H | 382_T | 1.805 | 1.00 |
| 70_A | 86_T | 1.801 | 1.00 |
| 318_V | 333_F | 1.800 | 1.00 |
| 201_S | 270_G | 1.770 | 1.00 |
| 185_R | 312_R | 1.761 | 1.00 |
| 69_C | 73_L | 1.742 | 1.00 |
| 30_C | 43_F | 1.738 | 1.00 |
| 331_F | 334_S | 1.726 | 1.00 |
| 396_A | 405_L | 1.704 | 1.00 |
| 164_P | 191_Q | 1.699 | 1.00 |
| 245_W | 412_Y | 1.660 | 1.00 |
| 106_Y | 110_E | 1.646 | 1.00 |
| 331_F | 359_Y | 1.644 | 1.00 |
| 189_R | 283_G | 1.639 | 1.00 |
| 286_P | 289_D | 1.615 | 1.00 |
| 262_D | 266_L | 1.596 | 1.00 |
| 135_L | 139_E | 1.586 | 1.00 |
| 240_C | 243_V | 1.574 | 1.00 |
| 355_V | 390_I | 1.573 | 1.00 |
| 183_F | 187_Q | 1.563 | 1.00 |
| 61_V | 65_T | 1.559 | 1.00 |
| 300_S | 362_H | 1.556 | 1.00 |
| 105_E | 108_L | 1.553 | 1.00 |
| 71_V | 75_C | 1.546 | 1.00 |
| 105_E | 109_H | 1.531 | 1.00 |
| 84_R | 88_C | 1.512 | 1.00 |
| 161_K | 164_P | 1.511 | 1.00 |
| 350_C | 402_L | 1.482 | 1.00 |
| 162_A | 166_F | 1.480 | 1.00 |
| 141_K | 184_Q | 1.472 | 1.00 |
| 73_L | 82_V | 1.468 | 1.00 |
| 328_L | 356_E | 1.468 | 1.00 |
| 107_Y | 336_W | 1.455 | 1.00 |
| 396_A | 406_W | 1.451 | 0.99 |
| 311_A | 315_R | 1.432 | 0.99 |
| 74_L | 137_I | 1.426 | 0.99 |
| 336_W | 349_V | 1.398 | 0.99 |
| 392_Y | 417_P | 1.395 | 0.99 |
| 289_D | 308_Q | 1.385 | 0.99 |
| 319_F | 326_P | 1.381 | 0.99 |
| 324_A | 364_F | 1.376 | 0.99 |
| 186_F | 190_V | 1.367 | 0.99 |
| 396_A | 409_C | 1.361 | 0.99 |
| 105_E | 115_R | 1.360 | 0.99 |
| 406_W | 410_N | 1.358 | 0.99 |
| 108_L | 112_P | 1.352 | 0.99 |
| 77_L | 82_V | 1.350 | 0.99 |
| 392_Y | 396_A | 1.347 | 0.99 |
| 72_A | 76_S | 1.341 | 0.99 |
| 74_L | 77_L | 1.334 | 0.99 |
| 255_Y | 394_M | 1.328 | 0.99 |
| 46_T | 50_A | 1.324 | 0.99 |
| 347_G | 399_V | 1.322 | 0.99 |
| 53_V | 60_A | 1.320 | 0.99 |
| 96_L | 116_F | 1.315 | 0.99 |
| 390_I | 394_M | 1.315 | 0.99 |
| 320_Q | 326_P | 1.307 | 0.99 |
| 386_T | 390_I | 1.304 | 0.99 |
| 299_I | 358_D | 1.297 | 0.99 |
| 87_F | 92_S | 1.288 | 0.99 |
| 320_Q | 323_R | 1.274 | 0.98 |
| 334_S | 351_W | 1.271 | 0.98 |
| 384_A | 388_L | 1.269 | 0.98 |
| 129_R | 181_C | 1.266 | 0.98 |
| 83_H | 87_F | 1.259 | 0.98 |
| 120_L | 176_L | 1.256 | 0.98 |
| 91_M | 333_F | 1.244 | 0.98 |
| 15_Y | 268_A | 1.239 | 0.98 |
| 395_L | 412_Y | 1.236 | 0.98 |
| 328_L | 360_L | 1.234 | 0.98 |
| 299_I | 386_T | 1.234 | 0.98 |
| 346_F | 349_V | 1.225 | 0.98 |
| 248_A | 395_L | 1.225 | 0.98 |
| 395_L | 409_C | 1.210 | 0.98 |
| 247_T | 408_L | 1.202 | 0.97 |
| 49_G | 170_L | 1.200 | 0.97 |
| 249_G | 391_A | 1.194 | 0.97 |
| 410_N | 414_S | 1.189 | 0.97 |
| 130_V | 165_Y | 1.188 | 0.97 |
| 354_M | 389_I | 1.188 | 0.97 |
| 402_L | 406_W | 1.187 | 0.97 |
| 244_V | 408_L | 1.182 | 0.97 |
| 49_G | 64_F | 1.179 | 0.97 |
| 319_F | 323_R | 1.179 | 0.97 |
| 88_C | 92_S | 1.178 | 0.97 |
| 355_V | 393_I | 1.175 | 0.97 |
| 65_T | 89_F | 1.175 | 0.97 |
| 255_Y | 294_E | 1.165 | 0.97 |
| 309_S | 312_R | 1.161 | 0.97 |
| 200_H | 208_R | 1.160 | 0.97 |
| 299_I | 390_I | 1.159 | 0.97 |
| 302_F | 394_M | 1.147 | 0.96 |
| 322_S | 329_Q | 1.142 | 0.96 |
| 290_I | 295_R | 1.135 | 0.96 |
| 248_A | 412_Y | 1.130 | 0.96 |
| 174_A | 181_C | 1.129 | 0.96 |
| 75_C | 160_C | 1.128 | 0.96 |
| 400_R | 404_S | 1.123 | 0.96 |
| 311_A | 327_L | 1.120 | 0.96 |
| 66_P | 93_W | 1.118 | 0.96 |
| 74_L | 133_L | 1.118 | 0.96 |
| 220_V | 258_H | 1.117 | 0.95 |
| 331_F | 355_V | 1.115 | 0.95 |
| 163_L | 167_S | 1.115 | 0.95 |
| 105_E | 116_F | 1.106 | 0.95 |
| 248_A | 408_L | 1.105 | 0.95 |
| 104_T | 108_L | 1.105 | 0.95 |
| 300_S | 304_R | 1.103 | 0.95 |
| 208_R | 212_I | 1.097 | 0.95 |
| 330_T | 334_S | 1.096 | 0.95 |
| 299_I | 355_V | 1.094 | 0.95 |
| 334_S | 359_Y | 1.085 | 0.94 |
| 185_R | 285_V | 1.085 | 0.94 |
| 297_H | 383_W | 1.078 | 0.94 |
| 327_L | 359_Y | 1.077 | 0.94 |
| 43_F | 47_G | 1.070 | 0.94 |
| 302_F | 390_I | 1.065 | 0.94 |
| 331_F | 356_E | 1.063 | 0.94 |
| 95_T | 107_Y | 1.063 | 0.94 |
| 66_P | 127_T | 1.061 | 0.94 |
| 45_L | 167_S | 1.061 | 0.94 |
| 70_A | 134_S | 1.060 | 0.94 |
| 387_Q | 391_A | 1.055 | 0.93 |
| 66_P | 130_V | 1.049 | 0.93 |
| 236_Q | 247_T | 1.048 | 0.93 |
| 242_Y | 246_T | 1.046 | 0.93 |
| 82_V | 85_W | 1.039 | 0.93 |
| 252_K | 294_E | 1.033 | 0.92 |
| 407_L | 411_S | 1.025 | 0.92 |
| 14_F | 18_A | 1.022 | 0.92 |
| 395_L | 405_L | 1.011 | 0.91 |
| 252_K | 387_Q | 1.009 | 0.91 |
| 67_A | 162_A | 1.008 | 0.91 |
| 320_Q | 351_W | 1.005 | 0.91 |
| 41_Y | 163_L | 1.001 | 0.91 |
| 322_S | 326_P | 1.000 | 0.91 |
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 | |
| 4n7wA | 2 | 0.3011 | 2.4 | 0.98 | Contact Map |
| 3wu2Z | 2 | 0.1425 | 1.3 | 0.983 | Contact Map |
| 3vouA | 2 | 0.1724 | 1.2 | 0.983 | Contact Map |
| 3zuxA | 1 | 0.2966 | 1.1 | 0.983 | Contact Map |
| 2l0lA | 1 | 0.0621 | 1.1 | 0.983 | Contact Map |
| 1sghB | 1 | 0.0299 | 1.1 | 0.983 | Contact Map |
| 3pfzA | 1 | 0.1356 | 1.1 | 0.983 | Contact Map |
| 4ogqE | 1 | 0.0713 | 1.1 | 0.984 | Contact Map |
| 1q90L | 1 | 0.0736 | 1 | 0.984 | Contact Map |
| 4ldsA | 2 | 0.3885 | 1 | 0.984 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)