| 1QOP_B |
| ID: | 1429468649 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 397 (390) | ||
| Sequences: | 4419 (2063.8) | ||
| Seq/Len: | 11.331 | ||
| Nf(neff/√len): | 104.5 |
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: 11.331).
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 |
| 123_S | 130_C | 4.686 | 1.00 |
| 212_T | 373_V | 4.590 | 1.00 |
| 251_G | 323_D | 4.355 | 1.00 |
| 331_E | 360_K | 3.837 | 1.00 |
| 61_K | 72_T | 3.219 | 1.00 |
| 136_A | 160_H | 3.019 | 1.00 |
| 227_V | 240_M | 2.844 | 1.00 |
| 32_F | 203_E | 2.794 | 1.00 |
| 226_A | 253_I | 2.759 | 1.00 |
| 260_H | 266_E | 2.721 | 1.00 |
| 72_T | 371_L | 2.689 | 1.00 |
| 12_F | 318_S | 2.684 | 1.00 |
| 258_G | 328_T | 2.572 | 1.00 |
| 129_K | 155_E | 2.520 | 1.00 |
| 191_A | 238_I | 2.492 | 1.00 |
| 131_R | 155_E | 2.469 | 1.00 |
| 59_L | 373_V | 2.446 | 1.00 |
| 328_T | 331_E | 2.427 | 1.00 |
| 176_D | 180_S | 2.422 | 1.00 |
| 206_R | 210_E | 2.419 | 1.00 |
| 133_Y | 176_D | 2.415 | 1.00 |
| 172_E | 175_R | 2.407 | 1.00 |
| 131_R | 157_I | 2.405 | 1.00 |
| 225_D | 370_Q | 2.315 | 1.00 |
| 105_E | 176_D | 2.279 | 1.00 |
| 51_N | 219_K | 2.204 | 1.00 |
| 136_A | 164_A | 2.200 | 1.00 |
| 227_V | 252_L | 2.154 | 1.00 |
| 61_K | 66_T | 2.147 | 1.00 |
| 255_V | 357_H | 2.124 | 1.00 |
| 271_L | 317_N | 2.099 | 1.00 |
| 209_G | 240_M | 2.036 | 1.00 |
| 68_G | 338_T | 2.022 | 1.00 |
| 150_R | 155_E | 1.987 | 1.00 |
| 61_K | 74_Y | 1.982 | 1.00 |
| 72_T | 220_E | 1.949 | 1.00 |
| 56_P | 214_A | 1.941 | 1.00 |
| 222_R | 371_L | 1.937 | 1.00 |
| 47_D | 51_N | 1.919 | 1.00 |
| 212_T | 240_M | 1.906 | 1.00 |
| 367_E | 370_Q | 1.861 | 1.00 |
| 57_T | 81_L | 1.857 | 1.00 |
| 63_Q | 67_A | 1.856 | 1.00 |
| 83_G | 121_L | 1.852 | 1.00 |
| 17_V | 25_L | 1.852 | 1.00 |
| 253_I | 323_D | 1.843 | 1.00 |
| 240_M | 375_N | 1.832 | 1.00 |
| 73_L | 358_A | 1.831 | 1.00 |
| 247_D | 250_V | 1.807 | 1.00 |
| 240_M | 252_L | 1.750 | 1.00 |
| 74_Y | 371_L | 1.740 | 1.00 |
| 338_T | 359_L | 1.737 | 1.00 |
| 265_G | 269_A | 1.706 | 1.00 |
| 259_G | 329_D | 1.698 | 1.00 |
| 335_A | 356_A | 1.698 | 1.00 |
| 75_L | 339_L | 1.692 | 1.00 |
| 31_A | 34_S | 1.676 | 1.00 |
| 22_M | 26_N | 1.655 | 1.00 |
| 227_V | 244_F | 1.651 | 1.00 |
| 214_A | 218_D | 1.651 | 1.00 |
| 95_A | 126_L | 1.625 | 1.00 |
| 254_G | 324_Y | 1.604 | 1.00 |
| 351_S | 377_S | 1.593 | 1.00 |
| 64_N | 67_A | 1.592 | 1.00 |
| 53_A | 81_L | 1.561 | 1.00 |
| 137_K | 140_E | 1.546 | 1.00 |
| 143_S | 147_F | 1.536 | 1.00 |
| 213_K | 247_D | 1.529 | 1.00 |
| 69_T | 359_L | 1.499 | 1.00 |
| 216_I | 373_V | 1.495 | 1.00 |
| 228_I | 358_A | 1.493 | 1.00 |
| 209_G | 243_D | 1.491 | 1.00 |
| 301_S | 332_A | 1.490 | 1.00 |
| 365_Q | 370_Q | 1.483 | 1.00 |
| 35_A | 100_R | 1.470 | 1.00 |
| 241_F | 320_G | 1.470 | 1.00 |
| 185_H | 197_Y | 1.450 | 1.00 |
| 337_K | 391_L | 1.436 | 1.00 |
| 325_V | 357_H | 1.419 | 1.00 |
| 15_M | 22_M | 1.417 | 1.00 |
| 29_E | 33_V | 1.415 | 1.00 |
| 356_A | 360_K | 1.414 | 1.00 |
| 163_S | 296_E | 1.413 | 1.00 |
| 144_P | 384_I | 1.410 | 1.00 |
| 270_P | 287_M | 1.406 | 0.99 |
| 336_F | 352_S | 1.406 | 0.99 |
| 333_L | 349_L | 1.405 | 0.99 |
| 226_A | 251_G | 1.404 | 0.99 |
| 245_I | 322_A | 1.399 | 0.99 |
| 39_P | 43_A | 1.387 | 0.99 |
| 175_R | 179_G | 1.381 | 0.99 |
| 338_T | 342_H | 1.377 | 0.99 |
| 313_H | 324_Y | 1.376 | 0.99 |
| 24_A | 181_Y | 1.375 | 0.99 |
| 116_G | 149_M | 1.370 | 0.99 |
| 72_T | 369_E | 1.369 | 0.99 |
| 56_P | 215_Q | 1.367 | 0.99 |
| 330_D | 334_E | 1.354 | 0.99 |
| 335_A | 355_L | 1.347 | 0.99 |
| 333_L | 390_I | 1.340 | 0.99 |
| 8_Y | 16_Y | 1.336 | 0.99 |
| 8_Y | 11_E | 1.334 | 0.99 |
| 357_H | 361_M | 1.331 | 0.99 |
| 304_L | 353_H | 1.327 | 0.99 |
| 237_A | 321_R | 1.306 | 0.99 |
| 226_A | 372_L | 1.300 | 0.99 |
| 35_A | 38_D | 1.300 | 0.99 |
| 11_E | 276_V | 1.296 | 0.99 |
| 285_P | 318_S | 1.293 | 0.99 |
| 147_F | 150_R | 1.287 | 0.99 |
| 216_I | 220_E | 1.286 | 0.99 |
| 3_T | 199_T | 1.273 | 0.99 |
| 68_G | 342_H | 1.268 | 0.99 |
| 228_I | 361_M | 1.267 | 0.99 |
| 111_G | 116_G | 1.254 | 0.99 |
| 64_N | 342_H | 1.247 | 0.99 |
| 216_I | 371_L | 1.244 | 0.98 |
| 354_A | 374_V | 1.238 | 0.98 |
| 220_E | 371_L | 1.233 | 0.98 |
| 121_L | 152_M | 1.232 | 0.98 |
| 327_I | 356_A | 1.231 | 0.98 |
| 33_V | 37_K | 1.222 | 0.98 |
| 52_Y | 92_L | 1.220 | 0.98 |
| 180_S | 183_T | 1.216 | 0.98 |
| 106_I | 123_S | 1.211 | 0.98 |
| 225_D | 371_L | 1.208 | 0.98 |
| 299_S | 305_D | 1.204 | 0.98 |
| 285_P | 317_N | 1.191 | 0.98 |
| 59_L | 216_I | 1.188 | 0.98 |
| 49_L | 53_A | 1.174 | 0.98 |
| 9_F | 199_T | 1.173 | 0.98 |
| 98_A | 101_M | 1.172 | 0.98 |
| 276_V | 283_K | 1.168 | 0.97 |
| 160_H | 164_A | 1.154 | 0.97 |
| 11_E | 318_S | 1.151 | 0.97 |
| 95_A | 106_I | 1.148 | 0.97 |
| 74_Y | 216_I | 1.139 | 0.97 |
| 15_M | 26_N | 1.138 | 0.97 |
| 279_Y | 284_A | 1.138 | 0.97 |
| 315_Y | 319_I | 1.133 | 0.97 |
| 224_P | 373_V | 1.129 | 0.97 |
| 228_I | 357_H | 1.127 | 0.97 |
| 62_C | 75_L | 1.121 | 0.97 |
| 331_E | 356_A | 1.120 | 0.96 |
| 73_L | 372_L | 1.119 | 0.96 |
| 339_L | 376_L | 1.115 | 0.96 |
| 273_H | 277_G | 1.114 | 0.96 |
| 350_E | 353_H | 1.113 | 0.96 |
| 35_A | 40_E | 1.102 | 0.96 |
| 74_Y | 220_E | 1.101 | 0.96 |
| 268_G | 272_K | 1.096 | 0.96 |
| 362_M | 372_L | 1.089 | 0.96 |
| 26_N | 30_E | 1.087 | 0.96 |
| 265_G | 273_H | 1.080 | 0.95 |
| 253_I | 361_M | 1.079 | 0.95 |
| 45_F | 49_L | 1.077 | 0.95 |
| 351_S | 376_L | 1.076 | 0.95 |
| 237_A | 317_N | 1.072 | 0.95 |
| 170_C | 192_A | 1.068 | 0.95 |
| 42_Q | 45_F | 1.065 | 0.95 |
| 336_F | 382_K | 1.062 | 0.95 |
| 26_N | 29_E | 1.060 | 0.95 |
| 60_T | 77_R | 1.051 | 0.94 |
| 149_M | 154_A | 1.044 | 0.94 |
| 32_F | 36_Q | 1.042 | 0.94 |
| 253_I | 325_V | 1.036 | 0.94 |
| 357_H | 360_K | 1.034 | 0.94 |
| 136_A | 139_V | 1.024 | 0.93 |
| 255_V | 325_V | 1.023 | 0.93 |
| 40_E | 43_A | 1.020 | 0.93 |
| 105_E | 129_K | 1.017 | 0.93 |
| 228_I | 255_V | 1.006 | 0.93 |
| 38_D | 100_R | 1.005 | 0.93 |
| 50_K | 218_D | 1.004 | 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 | |
| 4ht3B | 1 | 0.9874 | 100 | 0.247 | Contact Map |
| 4negA | 2 | 0.8161 | 100 | 0.25 | Contact Map |
| 1x1qA | 2 | 0.9647 | 100 | 0.253 | Contact Map |
| 2o2eA | 2 | 0.7935 | 100 | 0.255 | Contact Map |
| 1v8zA | 4 | 0.9723 | 100 | 0.269 | Contact Map |
| 3ss7X | 1 | 0.9194 | 100 | 0.356 | Contact Map |
| 1tdjA | 1 | 0.8237 | 100 | 0.36 | Contact Map |
| 2rkbA | 5 | 0.7783 | 100 | 0.368 | Contact Map |
| 2gn0A | 4 | 0.8186 | 100 | 0.38 | Contact Map |
| 1v71A | 1 | 0.796 | 100 | 0.38 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)