| H2 |
| ID: | 1508097374 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 435 (393) | ||
| Sequences: | 5697 (4335.5) | ||
| Seq/Len: | 14.496 | ||
| Nf(neff/√len): | 218.7 |
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: 14.496).
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 |
| 248_A | 391_A | 3.743 | 1.00 |
| 350_C | 393_I | 3.426 | 1.00 |
| 218_L | 260_I | 3.301 | 1.00 |
| 296_T | 301_V | 3.123 | 1.00 |
| 218_L | 256_Y | 3.088 | 1.00 |
| 354_M | 389_I | 3.002 | 1.00 |
| 78_A | 144_A | 2.960 | 1.00 |
| 211_Q | 275_L | 2.863 | 1.00 |
| 332_A | 349_V | 2.799 | 1.00 |
| 131_T | 135_L | 2.666 | 1.00 |
| 401_S | 404_S | 2.663 | 1.00 |
| 171_F | 266_L | 2.658 | 1.00 |
| 23_A | 47_G | 2.636 | 1.00 |
| 86_T | 134_S | 2.634 | 1.00 |
| 129_R | 174_A | 2.516 | 1.00 |
| 106_Y | 342_P | 2.451 | 1.00 |
| 256_Y | 260_I | 2.424 | 1.00 |
| 49_G | 67_A | 2.421 | 1.00 |
| 223_S | 226_V | 2.389 | 1.00 |
| 26_F | 43_F | 2.388 | 1.00 |
| 67_A | 166_F | 2.332 | 1.00 |
| 45_L | 166_F | 2.316 | 1.00 |
| 69_C | 89_F | 2.283 | 1.00 |
| 73_L | 86_T | 2.259 | 1.00 |
| 217_C | 221_A | 2.219 | 1.00 |
| 223_S | 227_D | 2.218 | 1.00 |
| 182_S | 316_R | 2.208 | 1.00 |
| 244_V | 391_A | 2.189 | 1.00 |
| 314_L | 334_S | 2.179 | 1.00 |
| 212_I | 261_L | 2.131 | 1.00 |
| 297_H | 301_V | 2.117 | 1.00 |
| 223_S | 229_G | 2.112 | 1.00 |
| 70_A | 90_Q | 2.110 | 1.00 |
| 267_H | 272_G | 2.088 | 1.00 |
| 314_L | 330_T | 2.075 | 1.00 |
| 207_W | 267_H | 2.047 | 1.00 |
| 294_E | 394_M | 2.036 | 1.00 |
| 224_R | 229_G | 2.031 | 1.00 |
| 245_W | 388_L | 1.999 | 1.00 |
| 185_R | 312_R | 1.978 | 1.00 |
| 274_E | 309_S | 1.946 | 1.00 |
| 30_C | 43_F | 1.872 | 1.00 |
| 346_F | 396_A | 1.864 | 1.00 |
| 44_L | 167_S | 1.857 | 1.00 |
| 392_Y | 409_C | 1.829 | 1.00 |
| 164_P | 191_Q | 1.827 | 1.00 |
| 68_V | 162_A | 1.807 | 1.00 |
| 211_Q | 263_D | 1.804 | 1.00 |
| 325_W | 329_Q | 1.803 | 1.00 |
| 224_R | 227_D | 1.800 | 1.00 |
| 161_K | 164_P | 1.795 | 1.00 |
| 84_R | 88_C | 1.790 | 1.00 |
| 350_C | 354_M | 1.775 | 1.00 |
| 241_I | 412_Y | 1.769 | 1.00 |
| 318_V | 333_F | 1.765 | 1.00 |
| 298_R | 358_D | 1.760 | 1.00 |
| 328_L | 349_V | 1.758 | 1.00 |
| 300_S | 359_Y | 1.732 | 1.00 |
| 383_W | 387_Q | 1.723 | 1.00 |
| 41_Y | 164_P | 1.723 | 1.00 |
| 76_S | 82_V | 1.722 | 1.00 |
| 297_H | 382_T | 1.719 | 1.00 |
| 66_P | 90_Q | 1.718 | 1.00 |
| 396_A | 405_L | 1.706 | 1.00 |
| 135_L | 139_E | 1.695 | 1.00 |
| 204_A | 272_G | 1.693 | 1.00 |
| 297_H | 379_R | 1.688 | 1.00 |
| 204_A | 267_H | 1.678 | 1.00 |
| 308_Q | 312_R | 1.664 | 1.00 |
| 132_S | 168_Y | 1.653 | 1.00 |
| 323_R | 359_Y | 1.645 | 1.00 |
| 130_V | 169_L | 1.641 | 1.00 |
| 225_V | 229_G | 1.615 | 1.00 |
| 101_L | 113_S | 1.612 | 1.00 |
| 189_R | 272_G | 1.552 | 1.00 |
| 351_W | 390_I | 1.550 | 1.00 |
| 223_S | 228_A | 1.547 | 1.00 |
| 183_F | 187_Q | 1.542 | 1.00 |
| 236_Q | 239_E | 1.512 | 1.00 |
| 70_A | 130_V | 1.511 | 1.00 |
| 399_V | 405_L | 1.511 | 1.00 |
| 79_P | 140_G | 1.505 | 1.00 |
| 328_L | 352_A | 1.502 | 1.00 |
| 300_S | 358_D | 1.500 | 1.00 |
| 400_R | 404_S | 1.494 | 1.00 |
| 23_A | 269_A | 1.488 | 1.00 |
| 73_L | 82_V | 1.486 | 1.00 |
| 275_L | 291_W | 1.480 | 1.00 |
| 331_F | 355_V | 1.466 | 1.00 |
| 74_L | 137_I | 1.463 | 1.00 |
| 162_A | 166_F | 1.461 | 1.00 |
| 69_C | 73_L | 1.453 | 1.00 |
| 53_V | 57_G | 1.443 | 1.00 |
| 224_R | 228_A | 1.428 | 1.00 |
| 336_W | 345_V | 1.408 | 1.00 |
| 226_V | 229_G | 1.406 | 0.99 |
| 299_I | 354_M | 1.401 | 0.99 |
| 70_A | 86_T | 1.374 | 0.99 |
| 72_A | 76_S | 1.368 | 0.99 |
| 83_H | 87_F | 1.367 | 0.99 |
| 74_L | 77_L | 1.359 | 0.99 |
| 208_R | 212_I | 1.355 | 0.99 |
| 396_A | 409_C | 1.354 | 0.99 |
| 390_I | 394_M | 1.350 | 0.99 |
| 49_G | 170_L | 1.340 | 0.99 |
| 61_V | 65_T | 1.331 | 0.99 |
| 231_G | 234_D | 1.330 | 0.99 |
| 263_D | 275_L | 1.330 | 0.99 |
| 343_G | 399_V | 1.319 | 0.99 |
| 53_V | 60_A | 1.314 | 0.99 |
| 346_F | 402_L | 1.313 | 0.99 |
| 141_K | 184_Q | 1.310 | 0.99 |
| 259_W | 263_D | 1.307 | 0.99 |
| 101_L | 115_R | 1.304 | 0.99 |
| 71_V | 75_C | 1.297 | 0.99 |
| 384_A | 388_L | 1.292 | 0.99 |
| 324_A | 360_L | 1.290 | 0.99 |
| 406_W | 410_N | 1.285 | 0.99 |
| 50_A | 54_A | 1.284 | 0.99 |
| 212_I | 268_A | 1.276 | 0.99 |
| 129_R | 181_C | 1.272 | 0.99 |
| 299_I | 386_T | 1.264 | 0.99 |
| 311_A | 315_R | 1.259 | 0.99 |
| 74_L | 133_L | 1.255 | 0.99 |
| 91_M | 333_F | 1.240 | 0.98 |
| 300_S | 304_R | 1.233 | 0.98 |
| 136_D | 317_L | 1.214 | 0.98 |
| 87_F | 92_S | 1.210 | 0.98 |
| 245_W | 391_A | 1.205 | 0.98 |
| 402_L | 406_W | 1.193 | 0.98 |
| 102_H | 106_Y | 1.192 | 0.98 |
| 396_A | 406_W | 1.192 | 0.98 |
| 297_H | 383_W | 1.185 | 0.98 |
| 159_V | 191_Q | 1.185 | 0.98 |
| 133_L | 160_C | 1.185 | 0.98 |
| 240_C | 408_L | 1.184 | 0.98 |
| 319_F | 326_P | 1.182 | 0.98 |
| 331_F | 334_S | 1.178 | 0.98 |
| 101_L | 114_V | 1.176 | 0.98 |
| 77_L | 82_V | 1.167 | 0.97 |
| 243_V | 408_L | 1.163 | 0.97 |
| 174_A | 181_C | 1.159 | 0.97 |
| 57_G | 61_V | 1.155 | 0.97 |
| 159_V | 164_P | 1.155 | 0.97 |
| 320_Q | 326_P | 1.153 | 0.97 |
| 250_L | 398_E | 1.148 | 0.97 |
| 379_R | 383_W | 1.145 | 0.97 |
| 292_T | 295_R | 1.144 | 0.97 |
| 331_F | 352_A | 1.141 | 0.97 |
| 291_W | 308_Q | 1.129 | 0.97 |
| 244_V | 395_L | 1.127 | 0.97 |
| 410_N | 414_S | 1.111 | 0.96 |
| 244_V | 412_Y | 1.111 | 0.96 |
| 322_S | 329_Q | 1.111 | 0.96 |
| 248_A | 387_Q | 1.110 | 0.96 |
| 332_A | 345_V | 1.108 | 0.96 |
| 251_F | 394_M | 1.107 | 0.96 |
| 205_L | 268_A | 1.101 | 0.96 |
| 205_L | 208_R | 1.100 | 0.96 |
| 101_L | 105_E | 1.099 | 0.96 |
| 240_C | 411_S | 1.096 | 0.96 |
| 350_C | 389_I | 1.095 | 0.96 |
| 311_A | 327_L | 1.095 | 0.96 |
| 96_L | 116_F | 1.095 | 0.96 |
| 302_F | 390_I | 1.091 | 0.96 |
| 66_P | 130_V | 1.088 | 0.96 |
| 186_F | 190_V | 1.087 | 0.96 |
| 302_F | 394_M | 1.083 | 0.96 |
| 208_R | 264_S | 1.083 | 0.96 |
| 324_A | 359_Y | 1.071 | 0.95 |
| 95_T | 103_Y | 1.070 | 0.95 |
| 215_L | 219_N | 1.067 | 0.95 |
| 43_F | 47_G | 1.063 | 0.95 |
| 219_N | 254_T | 1.059 | 0.95 |
| 103_Y | 336_W | 1.058 | 0.95 |
| 163_L | 167_S | 1.055 | 0.95 |
| 387_Q | 391_A | 1.053 | 0.95 |
| 351_W | 393_I | 1.053 | 0.95 |
| 299_I | 351_W | 1.049 | 0.94 |
| 390_I | 393_I | 1.040 | 0.94 |
| 407_L | 411_S | 1.036 | 0.94 |
| 361_I | 365_A | 1.033 | 0.94 |
| 96_L | 100_G | 1.031 | 0.94 |
| 12_I | 16_Q | 1.028 | 0.94 |
| 342_P | 345_V | 1.025 | 0.93 |
| 78_A | 143_K | 1.022 | 0.93 |
| 101_L | 104_T | 1.022 | 0.93 |
| 46_T | 50_A | 1.021 | 0.93 |
| 67_A | 70_A | 1.019 | 0.93 |
| 225_V | 228_A | 1.015 | 0.93 |
| 100_G | 104_T | 1.011 | 0.93 |
| 331_F | 351_W | 1.004 | 0.93 |
| 23_A | 27_N | 1.003 | 0.93 |
| 232_L | 235_C | 1.003 | 0.93 |
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 | |
| 2i2jA | 1 | 0.0483 | 2.4 | 0.978 | Contact Map |
| 1lbjA | 1 | 0.0506 | 2 | 0.979 | Contact Map |
| 2mbdA | 1 | 0.0414 | 1.6 | 0.98 | Contact Map |
| 1q90L | 1 | 0.0736 | 1.3 | 0.982 | Contact Map |
| 1jb0M | 1 | 0.0713 | 1.2 | 0.982 | Contact Map |
| 1rmkA | 1 | 0.0713 | 1.1 | 0.982 | Contact Map |
| 4ogqE | 1 | 0.0713 | 1.1 | 0.982 | Contact Map |
| 4ujpB | 1 | 0.0345 | 1.1 | 0.982 | Contact Map |
| 2mc7A | 1 | 0.069 | 1 | 0.983 | Contact Map |
| 2le3A | 1 | 0.0966 | 1 | 0.983 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)