| antitrypsin_try |
| ID: | 1475584307 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 394 (370) | ||
| Sequences: | 2738 (1801) | ||
| Seq/Len: | 7.400 | ||
| Nf(neff/√len): | 93.6 |
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: 7.400).
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 |
| 75_E | 310_K | 4.610 | 1.00 |
| 311_V | 318_L | 4.017 | 1.00 |
| 205_E | 219_P | 3.816 | 1.00 |
| 244_Y | 345_T | 3.741 | 1.00 |
| 75_E | 309_T | 3.000 | 1.00 |
| 240_L | 286_L | 2.830 | 1.00 |
| 298_D | 331_K | 2.754 | 1.00 |
| 162_E | 170_V | 2.705 | 1.00 |
| 292_S | 339_T | 2.690 | 1.00 |
| 69_K | 320_G | 2.613 | 1.00 |
| 252_F | 366_F | 2.604 | 1.00 |
| 207_D | 217_K | 2.542 | 1.00 |
| 76_I | 308_I | 2.535 | 1.00 |
| 57_I | 334_H | 2.520 | 1.00 |
| 71_D | 310_K | 2.487 | 1.00 |
| 145_V | 153_A | 2.461 | 1.00 |
| 264_E | 387_K | 2.361 | 1.00 |
| 288_L | 366_F | 2.319 | 1.00 |
| 93_H | 138_Y | 2.306 | 1.00 |
| 228_N | 241_L | 2.209 | 1.00 |
| 252_F | 288_L | 2.139 | 1.00 |
| 338_L | 372_F | 2.132 | 1.00 |
| 223_R | 227_F | 2.129 | 1.00 |
| 300_K | 331_K | 2.115 | 1.00 |
| 372_F | 386_G | 2.093 | 1.00 |
| 38_Y | 264_E | 2.012 | 1.00 |
| 146_N | 149_D | 1.981 | 1.00 |
| 300_K | 304_G | 1.966 | 1.00 |
| 154_K | 173_V | 1.945 | 1.00 |
| 241_L | 377_Q | 1.933 | 1.00 |
| 285_S | 363_E | 1.929 | 1.00 |
| 291_L | 340_I | 1.911 | 1.00 |
| 154_K | 174_K | 1.892 | 1.00 |
| 241_L | 249_T | 1.879 | 1.00 |
| 286_L | 366_F | 1.861 | 1.00 |
| 205_E | 217_K | 1.833 | 1.00 |
| 222_K | 287_H | 1.829 | 1.00 |
| 194_W | 198_F | 1.796 | 1.00 |
| 250_A | 374_M | 1.763 | 1.00 |
| 287_H | 365_K | 1.761 | 1.00 |
| 72_T | 311_V | 1.732 | 1.00 |
| 63_M | 134_V | 1.712 | 1.00 |
| 294_T | 335_K | 1.703 | 1.00 |
| 30_L | 58_A | 1.699 | 1.00 |
| 296_T | 335_K | 1.694 | 1.00 |
| 162_E | 167_G | 1.643 | 1.00 |
| 207_D | 215_T | 1.641 | 1.00 |
| 236_S | 256_D | 1.633 | 1.00 |
| 65_S | 77_L | 1.620 | 1.00 |
| 173_V | 176_L | 1.606 | 1.00 |
| 165_T | 169_I | 1.601 | 1.00 |
| 135_K | 141_E | 1.592 | 1.00 |
| 242_M | 288_L | 1.589 | 1.00 |
| 206_E | 287_H | 1.578 | 1.00 |
| 314_N | 328_K | 1.536 | 1.00 |
| 373_L | 385_M | 1.531 | 1.00 |
| 120_L | 126_L | 1.531 | 1.00 |
| 206_E | 220_M | 1.527 | 1.00 |
| 128_D | 132_E | 1.520 | 0.99 |
| 209_H | 215_T | 1.517 | 0.99 |
| 173_V | 352_F | 1.515 | 0.99 |
| 66_L | 93_H | 1.496 | 0.99 |
| 311_V | 329_L | 1.486 | 0.99 |
| 60_A | 353_L | 1.484 | 0.99 |
| 155_K | 159_D | 1.475 | 0.99 |
| 241_L | 251_I | 1.473 | 0.99 |
| 290_K | 342_E | 1.468 | 0.99 |
| 119_F | 185_V | 1.467 | 0.99 |
| 161_V | 172_L | 1.466 | 0.99 |
| 318_L | 329_L | 1.461 | 0.99 |
| 366_F | 388_V | 1.450 | 0.99 |
| 38_Y | 385_M | 1.449 | 0.99 |
| 198_F | 221_M | 1.440 | 0.99 |
| 203_T | 221_M | 1.432 | 0.99 |
| 231_H | 256_D | 1.431 | 0.99 |
| 290_K | 341_D | 1.430 | 0.99 |
| 376_E | 379_T | 1.430 | 0.99 |
| 250_A | 340_I | 1.428 | 0.99 |
| 197_P | 343_K | 1.425 | 0.99 |
| 64_L | 318_L | 1.416 | 0.99 |
| 198_F | 203_T | 1.415 | 0.99 |
| 61_F | 303_L | 1.403 | 0.99 |
| 115_G | 187_Y | 1.396 | 0.99 |
| 64_L | 138_Y | 1.390 | 0.99 |
| 60_A | 334_H | 1.389 | 0.99 |
| 240_L | 364_V | 1.384 | 0.99 |
| 172_L | 350_A | 1.369 | 0.99 |
| 253_F | 373_L | 1.368 | 0.99 |
| 53_S | 56_S | 1.344 | 0.98 |
| 158_N | 165_T | 1.320 | 0.98 |
| 249_T | 377_Q | 1.319 | 0.98 |
| 115_G | 160_Y | 1.318 | 0.98 |
| 65_S | 76_I | 1.313 | 0.98 |
| 65_S | 73_H | 1.309 | 0.98 |
| 159_D | 163_K | 1.295 | 0.98 |
| 51_F | 336_A | 1.283 | 0.98 |
| 113_T | 166_Q | 1.273 | 0.98 |
| 64_L | 329_L | 1.263 | 0.97 |
| 254_L | 364_V | 1.242 | 0.97 |
| 254_L | 368_K | 1.239 | 0.97 |
| 293_I | 372_F | 1.238 | 0.97 |
| 322_T | 327_L | 1.227 | 0.97 |
| 332_A | 353_L | 1.227 | 0.97 |
| 347_A | 351_M | 1.219 | 0.97 |
| 67_G | 321_V | 1.218 | 0.97 |
| 340_I | 345_T | 1.218 | 0.97 |
| 342_E | 347_A | 1.216 | 0.97 |
| 129_K | 133_D | 1.214 | 0.97 |
| 51_F | 338_L | 1.202 | 0.96 |
| 203_T | 342_E | 1.200 | 0.96 |
| 308_I | 311_V | 1.198 | 0.96 |
| 194_W | 221_M | 1.197 | 0.96 |
| 151_E | 154_K | 1.197 | 0.96 |
| 291_L | 338_L | 1.188 | 0.96 |
| 188_I | 384_F | 1.187 | 0.96 |
| 79_G | 308_I | 1.178 | 0.96 |
| 221_M | 342_E | 1.161 | 0.95 |
| 347_A | 350_A | 1.159 | 0.95 |
| 191_K | 343_K | 1.158 | 0.95 |
| 388_V | 391_P | 1.156 | 0.95 |
| 286_L | 364_V | 1.156 | 0.95 |
| 161_V | 165_T | 1.147 | 0.95 |
| 344_G | 348_A | 1.146 | 0.95 |
| 239_V | 275_F | 1.137 | 0.94 |
| 210_V | 391_P | 1.131 | 0.94 |
| 216_V | 219_P | 1.130 | 0.94 |
| 258_G | 368_K | 1.128 | 0.94 |
| 40_Q | 305_Q | 1.127 | 0.94 |
| 188_I | 336_A | 1.118 | 0.94 |
| 56_S | 186_N | 1.115 | 0.94 |
| 374_M | 384_F | 1.115 | 0.94 |
| 194_W | 344_G | 1.115 | 0.94 |
| 200_V | 343_K | 1.114 | 0.94 |
| 193_K | 245_L | 1.104 | 0.93 |
| 198_F | 208_F | 1.103 | 0.93 |
| 310_K | 317_D | 1.103 | 0.93 |
| 227_F | 286_L | 1.102 | 0.93 |
| 259_K | 368_K | 1.100 | 0.93 |
| 307_G | 351_M | 1.099 | 0.93 |
| 116_N | 186_N | 1.098 | 0.93 |
| 30_L | 34_A | 1.097 | 0.93 |
| 238_W | 364_V | 1.094 | 0.93 |
| 162_E | 171_D | 1.091 | 0.93 |
| 57_I | 299_L | 1.091 | 0.93 |
| 147_F | 153_A | 1.090 | 0.93 |
| 203_T | 208_F | 1.084 | 0.92 |
| 387_K | 391_P | 1.081 | 0.92 |
| 176_L | 183_A | 1.080 | 0.92 |
| 364_V | 370_F | 1.079 | 0.92 |
| 227_F | 240_L | 1.079 | 0.92 |
| 344_G | 347_A | 1.078 | 0.92 |
| 66_L | 138_Y | 1.074 | 0.92 |
| 342_E | 345_T | 1.073 | 0.92 |
| 69_K | 317_D | 1.072 | 0.92 |
| 230_Q | 241_L | 1.066 | 0.92 |
| 38_Y | 387_K | 1.063 | 0.91 |
| 260_L | 263_L | 1.058 | 0.91 |
| 121_S | 148_G | 1.057 | 0.91 |
| 158_N | 161_V | 1.057 | 0.91 |
| 193_K | 197_P | 1.054 | 0.91 |
| 117_G | 160_Y | 1.053 | 0.91 |
| 32_E | 36_S | 1.053 | 0.91 |
| 127_V | 323_E | 1.048 | 0.91 |
| 347_A | 384_F | 1.048 | 0.91 |
| 237_S | 253_F | 1.037 | 0.90 |
| 203_T | 220_M | 1.035 | 0.90 |
| 36_S | 81_N | 1.032 | 0.90 |
| 67_G | 130_F | 1.030 | 0.90 |
| 174_K | 333_V | 1.030 | 0.90 |
| 206_E | 365_K | 1.026 | 0.89 |
| 122_E | 146_N | 1.025 | 0.89 |
| 224_L | 283_S | 1.024 | 0.89 |
| 238_W | 256_D | 1.022 | 0.89 |
| 72_T | 316_A | 1.020 | 0.89 |
| 130_F | 153_A | 1.019 | 0.89 |
| 199_E | 202_D | 1.019 | 0.89 |
| 210_V | 216_V | 1.016 | 0.89 |
| 30_L | 33_F | 1.008 | 0.88 |
| 337_V | 346_E | 1.007 | 0.88 |
| 229_I | 238_W | 1.007 | 0.88 |
| 31_A | 382_P | 1.004 | 0.88 |
| 308_I | 318_L | 1.002 | 0.88 |
| 291_L | 372_F | 1.002 | 0.88 |
| 304_G | 309_T | 1.000 | 0.88 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3ne4A | 1 | 0.9391 | 100 | 0.061 | Contact Map |
| 4c41A | 1 | 0.9315 | 100 | 0.086 | Contact Map |
| 2ceoA | 2 | 0.9264 | 100 | 0.087 | Contact Map |
| 1qmnA | 1 | 0.9112 | 100 | 0.09 | Contact Map |
| 1yxaA | 2 | 0.9442 | 100 | 0.09 | Contact Map |
| 4if8A | 2 | 0.9365 | 100 | 0.098 | Contact Map |
| 2v95A | 1 | 0.868 | 100 | 0.1 | Contact Map |
| 3f5nA | 5 | 0.9213 | 100 | 0.103 | Contact Map |
| 1uhgA | 4 | 0.9239 | 100 | 0.103 | Contact Map |
| 3b9fI | 1 | 0.8959 | 100 | 0.104 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)