| 3gia |
| ID: | 1380612533 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 444 (416) | ||
| Sequences: | 11208 (7160.5) | ||
| Seq/Len: | 26.942 | ||
| Nf(neff/√len): | 351.1 |
HHblits Results: (2013_03)
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: 26.942).
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 |
| 311_F | 322_E | 4.184 | 1.00 |
| 137_T | 328_S | 3.528 | 1.00 |
| 356_L | 380_F | 3.259 | 1.00 |
| 169_G | 242_S | 3.156 | 1.00 |
| 219_K | 223_R | 2.985 | 1.00 |
| 303_A | 313_E | 2.940 | 1.00 |
| 9_S | 215_E | 2.800 | 1.00 |
| 49_G | 233_M | 2.695 | 1.00 |
| 216_N | 219_K | 2.635 | 1.00 |
| 130_I | 335_A | 2.536 | 1.00 |
| 167_F | 171_I | 2.493 | 1.00 |
| 306_G | 310_E | 2.490 | 1.00 |
| 325_Y | 329_A | 2.411 | 1.00 |
| 14_V | 227_I | 2.383 | 1.00 |
| 377_I | 381_I | 2.366 | 1.00 |
| 300_Y | 304_K | 2.362 | 1.00 |
| 359_I | 379_S | 2.344 | 1.00 |
| 73_I | 305_D | 2.339 | 1.00 |
| 214_I | 220_N | 2.333 | 1.00 |
| 10_L | 227_I | 2.202 | 1.00 |
| 80_I | 364_I | 2.185 | 1.00 |
| 212_E | 304_K | 2.138 | 1.00 |
| 10_L | 220_N | 2.097 | 1.00 |
| 58_S | 359_I | 2.094 | 1.00 |
| 248_P | 251_E | 2.075 | 1.00 |
| 312_F | 326_I | 2.073 | 1.00 |
| 364_I | 367_D | 2.045 | 1.00 |
| 360_L | 380_F | 2.019 | 1.00 |
| 213_H | 297_N | 1.997 | 1.00 |
| 268_L | 272_G | 1.985 | 1.00 |
| 364_I | 368_E | 1.983 | 1.00 |
| 251_E | 266_P | 1.936 | 1.00 |
| 130_I | 332_V | 1.926 | 1.00 |
| 314_R | 317_W | 1.920 | 1.00 |
| 9_S | 12_E | 1.905 | 1.00 |
| 137_T | 324_L | 1.890 | 1.00 |
| 271_L | 275_L | 1.886 | 1.00 |
| 77_H | 82_D | 1.885 | 1.00 |
| 80_I | 360_L | 1.874 | 1.00 |
| 50_I | 378_F | 1.867 | 1.00 |
| 13_A | 214_I | 1.854 | 1.00 |
| 90_S | 302_L | 1.852 | 1.00 |
| 141_F | 325_Y | 1.835 | 1.00 |
| 10_L | 14_V | 1.828 | 1.00 |
| 141_F | 321_T | 1.815 | 1.00 |
| 314_R | 322_E | 1.813 | 1.00 |
| 94_W | 327_T | 1.797 | 1.00 |
| 50_I | 54_L | 1.776 | 1.00 |
| 145_K | 149_R | 1.769 | 1.00 |
| 138_A | 142_F | 1.765 | 1.00 |
| 363_Y | 377_I | 1.730 | 1.00 |
| 156_L | 160_L | 1.726 | 1.00 |
| 159_L | 163_G | 1.698 | 1.00 |
| 216_N | 223_R | 1.689 | 1.00 |
| 223_R | 227_I | 1.683 | 1.00 |
| 87_G | 91_I | 1.682 | 1.00 |
| 83_N | 421_K | 1.677 | 1.00 |
| 40_N | 190_M | 1.665 | 1.00 |
| 134_A | 332_V | 1.665 | 1.00 |
| 77_H | 86_T | 1.656 | 1.00 |
| 374_E | 378_F | 1.646 | 1.00 |
| 89_L | 357_F | 1.633 | 1.00 |
| 33_G | 41_L | 1.617 | 1.00 |
| 61_K | 366_I | 1.609 | 1.00 |
| 44_T | 193_A | 1.606 | 1.00 |
| 12_E | 152_F | 1.602 | 1.00 |
| 226_F | 230_L | 1.602 | 1.00 |
| 8_L | 12_E | 1.592 | 1.00 |
| 381_I | 385_G | 1.583 | 1.00 |
| 140_N | 289_N | 1.579 | 1.00 |
| 160_L | 164_L | 1.567 | 1.00 |
| 46_I | 237_V | 1.548 | 1.00 |
| 14_V | 231_I | 1.542 | 1.00 |
| 83_N | 86_T | 1.528 | 1.00 |
| 311_F | 314_R | 1.523 | 1.00 |
| 56_A | 229_I | 1.510 | 1.00 |
| 101_I | 331_G | 1.503 | 1.00 |
| 230_L | 234_F | 1.500 | 1.00 |
| 81_G | 422_V | 1.494 | 1.00 |
| 322_E | 326_I | 1.493 | 1.00 |
| 216_N | 220_N | 1.493 | 1.00 |
| 76_I | 357_F | 1.486 | 1.00 |
| 217_P | 222_P | 1.484 | 1.00 |
| 133_V | 331_G | 1.478 | 1.00 |
| 316_V | 321_T | 1.456 | 1.00 |
| 299_A | 308_L | 1.456 | 1.00 |
| 316_V | 319_K | 1.443 | 1.00 |
| 34_A | 41_L | 1.438 | 1.00 |
| 262_V | 266_P | 1.432 | 1.00 |
| 362_H | 376_V | 1.431 | 1.00 |
| 310_E | 313_E | 1.423 | 1.00 |
| 295_G | 327_T | 1.417 | 1.00 |
| 210_A | 293_Y | 1.416 | 1.00 |
| 296_A | 324_L | 1.415 | 1.00 |
| 299_A | 323_G | 1.411 | 1.00 |
| 69_N | 212_E | 1.404 | 0.99 |
| 21_M | 232_V | 1.404 | 0.99 |
| 362_H | 366_I | 1.395 | 0.99 |
| 105_A | 288_M | 1.392 | 0.99 |
| 58_S | 376_V | 1.383 | 0.99 |
| 112_F | 128_T | 1.379 | 0.99 |
| 66_I | 78_K | 1.376 | 0.99 |
| 274_L | 278_I | 1.369 | 0.99 |
| 380_F | 384_L | 1.355 | 0.99 |
| 169_G | 246_N | 1.349 | 0.99 |
| 134_A | 328_S | 1.345 | 0.99 |
| 269_G | 272_G | 1.339 | 0.99 |
| 166_I | 238_G | 1.332 | 0.99 |
| 10_L | 223_R | 1.332 | 0.99 |
| 170_L | 242_S | 1.331 | 0.99 |
| 74_A | 78_K | 1.328 | 0.99 |
| 126_A | 130_I | 1.326 | 0.99 |
| 130_I | 134_A | 1.325 | 0.99 |
| 8_L | 148_G | 1.317 | 0.99 |
| 28_S | 107_G | 1.316 | 0.99 |
| 108_F | 281_L | 1.305 | 0.99 |
| 18_V | 231_I | 1.305 | 0.99 |
| 314_R | 319_K | 1.299 | 0.99 |
| 63_G | 75_F | 1.294 | 0.99 |
| 17_A | 228_S | 1.293 | 0.99 |
| 105_A | 133_V | 1.292 | 0.99 |
| 137_T | 325_Y | 1.289 | 0.99 |
| 76_I | 89_L | 1.288 | 0.99 |
| 48_S | 197_F | 1.278 | 0.99 |
| 356_L | 384_L | 1.273 | 0.99 |
| 136_F | 288_M | 1.266 | 0.99 |
| 56_A | 225_I | 1.261 | 0.99 |
| 265_K | 273_F | 1.258 | 0.99 |
| 371_G | 375_I | 1.257 | 0.99 |
| 220_N | 223_R | 1.255 | 0.99 |
| 315_K | 319_K | 1.245 | 0.98 |
| 55_V | 359_I | 1.240 | 0.98 |
| 329_A | 333_L | 1.235 | 0.98 |
| 360_L | 364_I | 1.231 | 0.98 |
| 79_A | 361_S | 1.228 | 0.98 |
| 262_V | 265_K | 1.228 | 0.98 |
| 42_P | 241_I | 1.224 | 0.98 |
| 137_T | 141_F | 1.221 | 0.98 |
| 144_S | 293_Y | 1.215 | 0.98 |
| 8_L | 13_A | 1.209 | 0.98 |
| 373_K | 377_I | 1.205 | 0.98 |
| 161_I | 279_G | 1.200 | 0.98 |
| 129_E | 335_A | 1.196 | 0.98 |
| 61_K | 64_A | 1.196 | 0.98 |
| 133_V | 328_S | 1.194 | 0.98 |
| 373_K | 376_V | 1.194 | 0.98 |
| 304_K | 313_E | 1.193 | 0.98 |
| 163_G | 167_F | 1.188 | 0.98 |
| 363_Y | 367_D | 1.176 | 0.98 |
| 356_L | 360_L | 1.172 | 0.98 |
| 322_E | 325_Y | 1.170 | 0.97 |
| 12_E | 149_R | 1.168 | 0.97 |
| 68_S | 74_A | 1.166 | 0.97 |
| 91_I | 308_L | 1.160 | 0.97 |
| 419_Y | 423_T | 1.160 | 0.97 |
| 205_G | 209_N | 1.141 | 0.97 |
| 416_E | 420_R | 1.133 | 0.97 |
| 234_F | 238_G | 1.126 | 0.97 |
| 84_I | 88_A | 1.126 | 0.97 |
| 59_Y | 72_P | 1.125 | 0.97 |
| 164_L | 168_A | 1.119 | 0.96 |
| 96_S | 351_F | 1.116 | 0.96 |
| 202_M | 351_F | 1.108 | 0.96 |
| 317_W | 321_T | 1.104 | 0.96 |
| 127_I | 131_G | 1.104 | 0.96 |
| 412_V | 415_F | 1.103 | 0.96 |
| 83_N | 87_G | 1.101 | 0.96 |
| 70_A | 73_I | 1.100 | 0.96 |
| 73_I | 301_S | 1.099 | 0.96 |
| 11_W | 149_R | 1.096 | 0.96 |
| 112_F | 281_L | 1.095 | 0.96 |
| 76_I | 361_S | 1.091 | 0.96 |
| 415_F | 419_Y | 1.088 | 0.96 |
| 11_W | 15_S | 1.085 | 0.96 |
| 49_G | 201_Y | 1.081 | 0.95 |
| 102_A | 343_V | 1.081 | 0.95 |
| 94_W | 299_A | 1.079 | 0.95 |
| 265_K | 270_N | 1.076 | 0.95 |
| 33_G | 37_A | 1.076 | 0.95 |
| 371_G | 374_E | 1.074 | 0.95 |
| 150_A | 154_I | 1.074 | 0.95 |
| 81_G | 85_I | 1.070 | 0.95 |
| 46_I | 50_I | 1.065 | 0.95 |
| 314_R | 321_T | 1.063 | 0.95 |
| 87_G | 90_S | 1.062 | 0.95 |
| 151_E | 289_N | 1.061 | 0.95 |
| 159_L | 235_V | 1.054 | 0.95 |
| 17_A | 207_I | 1.054 | 0.95 |
| 138_A | 141_F | 1.052 | 0.95 |
| 361_S | 365_L | 1.052 | 0.95 |
| 211_S | 221_V | 1.045 | 0.94 |
| 80_I | 85_I | 1.044 | 0.94 |
| 149_R | 153_F | 1.040 | 0.94 |
| 388_L | 392_Y | 1.040 | 0.94 |
| 141_F | 319_K | 1.038 | 0.94 |
| 292_I | 296_A | 1.035 | 0.94 |
| 374_E | 377_I | 1.033 | 0.94 |
| 139_L | 150_A | 1.033 | 0.94 |
| 16_M | 210_A | 1.033 | 0.94 |
| 13_A | 224_A | 1.025 | 0.93 |
| 165_F | 169_G | 1.022 | 0.93 |
| 134_A | 138_A | 1.022 | 0.93 |
| 92_L | 354_I | 1.019 | 0.93 |
| 166_I | 169_G | 1.017 | 0.93 |
| 103_L | 199_L | 1.017 | 0.93 |
| 54_L | 378_F | 1.014 | 0.93 |
| 7_K | 145_K | 1.009 | 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 | |
| 3giaA | 1 | 0.9752 | 100 | 0.183 | Contact Map |
| 3l1lA | 1 | 0.9234 | 100 | 0.324 | Contact Map |
| 4djkA | 2 | 0.9189 | 100 | 0.406 | Contact Map |
| 2jlnA | 1 | 0.8986 | 99.6 | 0.803 | Contact Map |
| 3dh4A | 4 | 0.9347 | 98.8 | 0.868 | Contact Map |
| 2xq2A | 1 | 0.9369 | 98.8 | 0.868 | Contact Map |
| 4m48A | 1 | 0.9302 | 96.4 | 0.92 | Contact Map |
| 2a65A | 1 | 0.9167 | 96.3 | 0.921 | Contact Map |
| 4c7rA | 3 | 0.8874 | 93 | 0.934 | Contact Map |
| 2wswA | 1 | 0.7928 | 73 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)