| 1xqf |
| ID: | 1408344871 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 384 (382) | ||
| Sequences: | 2667 (1704.4) | ||
| Seq/Len: | 6.982 | ||
| Nf(neff/√len): | 87.2 |
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: 6.982).
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 |
| 175_V | 365_G | 5.113 | 1.00 |
| 20_F | 205_I | 4.519 | 1.00 |
| 322_V | 326_M | 4.067 | 1.00 |
| 373_K | 376_D | 3.792 | 1.00 |
| 277_I | 285_I | 3.274 | 1.00 |
| 176_G | 372_Y | 3.251 | 1.00 |
| 269_G | 289_A | 3.037 | 1.00 |
| 60_Y | 135_T | 2.984 | 1.00 |
| 242_G | 287_V | 2.976 | 1.00 |
| 150_L | 359_I | 2.953 | 1.00 |
| 248_W | 254_P | 2.817 | 1.00 |
| 325_I | 354_L | 2.794 | 1.00 |
| 97_I | 226_A | 2.754 | 1.00 |
| 203_T | 260_C | 2.689 | 1.00 |
| 351_L | 355_E | 2.630 | 1.00 |
| 321_I | 357_I | 2.472 | 1.00 |
| 144_M | 150_L | 2.471 | 1.00 |
| 211_F | 233_V | 2.469 | 1.00 |
| 59_V | 80_M | 2.440 | 1.00 |
| 215_A | 229_F | 2.413 | 1.00 |
| 51_A | 240_I | 2.384 | 1.00 |
| 296_G | 318_V | 2.363 | 1.00 |
| 288_V | 322_V | 2.323 | 1.00 |
| 15_T | 100_A | 2.319 | 1.00 |
| 326_M | 329_I | 2.311 | 1.00 |
| 156_A | 356_S | 2.266 | 1.00 |
| 293_G | 319_C | 2.251 | 1.00 |
| 81_L | 99_V | 2.215 | 1.00 |
| 240_I | 263_A | 2.210 | 1.00 |
| 163_T | 324_C | 2.188 | 1.00 |
| 369_F | 373_K | 2.151 | 1.00 |
| 117_L | 121_I | 2.109 | 1.00 |
| 66_F | 98_H | 2.068 | 1.00 |
| 270_V | 277_I | 2.016 | 1.00 |
| 179_L | 369_F | 1.995 | 1.00 |
| 240_I | 259_A | 1.989 | 1.00 |
| 227_L | 231_N | 1.927 | 1.00 |
| 141_I | 168_N | 1.866 | 1.00 |
| 292_A | 322_V | 1.866 | 1.00 |
| 373_K | 377_L | 1.864 | 1.00 |
| 65_A | 142_A | 1.861 | 1.00 |
| 238_A | 283_L | 1.831 | 1.00 |
| 54_C | 103_G | 1.824 | 1.00 |
| 14_C | 216_G | 1.793 | 1.00 |
| 128_I | 379_V | 1.786 | 1.00 |
| 55_I | 283_L | 1.779 | 1.00 |
| 33_L | 257_L | 1.749 | 1.00 |
| 199_V | 260_C | 1.736 | 1.00 |
| 157_L | 275_G | 1.735 | 1.00 |
| 56_L | 131_V | 1.735 | 1.00 |
| 46_V | 114_V | 1.733 | 1.00 |
| 137_S | 367_V | 1.733 | 1.00 |
| 170_A | 317_G | 1.706 | 1.00 |
| 64_L | 73_F | 1.673 | 1.00 |
| 141_I | 360_T | 1.670 | 1.00 |
| 53_V | 134_L | 1.656 | 1.00 |
| 144_M | 359_I | 1.645 | 1.00 |
| 122_R | 380_G | 1.639 | 1.00 |
| 172_A | 364_S | 1.637 | 1.00 |
| 296_G | 314_G | 1.632 | 1.00 |
| 54_C | 233_V | 1.607 | 1.00 |
| 200_F | 256_L | 1.602 | 1.00 |
| 112_L | 312_V | 1.594 | 1.00 |
| 363_W | 367_V | 1.578 | 1.00 |
| 234_V | 283_L | 1.560 | 1.00 |
| 56_L | 139_I | 1.552 | 1.00 |
| 99_V | 230_V | 1.551 | 1.00 |
| 110_V | 130_V | 1.534 | 0.99 |
| 354_L | 358_A | 1.526 | 0.99 |
| 325_I | 350_L | 1.520 | 0.99 |
| 177_A | 306_V | 1.508 | 0.99 |
| 56_L | 135_T | 1.495 | 0.99 |
| 322_V | 329_I | 1.485 | 0.99 |
| 41_S | 45_Q | 1.468 | 0.99 |
| 269_G | 285_I | 1.468 | 0.99 |
| 167_I | 171_I | 1.467 | 0.99 |
| 49_T | 126_V | 1.467 | 0.99 |
| 171_I | 365_G | 1.454 | 0.99 |
| 8_N | 97_I | 1.452 | 0.99 |
| 264_I | 315_V | 1.449 | 0.99 |
| 48_V | 127_L | 1.445 | 0.99 |
| 117_L | 176_G | 1.438 | 0.99 |
| 171_I | 175_V | 1.433 | 0.99 |
| 151_L | 356_S | 1.430 | 0.99 |
| 10_F | 13_I | 1.422 | 0.99 |
| 116_A | 173_G | 1.412 | 0.99 |
| 195_N | 198_M | 1.411 | 0.99 |
| 306_V | 314_G | 1.401 | 0.99 |
| 78_W | 95_Q | 1.388 | 0.99 |
| 58_V | 234_V | 1.381 | 0.99 |
| 128_I | 375_A | 1.378 | 0.99 |
| 376_D | 380_G | 1.369 | 0.98 |
| 154_H | 355_E | 1.364 | 0.98 |
| 343_G | 346_M | 1.355 | 0.98 |
| 45_Q | 114_V | 1.353 | 0.98 |
| 44_T | 259_A | 1.347 | 0.98 |
| 19_L | 208_I | 1.335 | 0.98 |
| 350_L | 354_L | 1.331 | 0.98 |
| 19_L | 50_F | 1.325 | 0.98 |
| 125_A | 375_A | 1.325 | 0.98 |
| 10_F | 14_C | 1.320 | 0.98 |
| 196_L | 257_L | 1.319 | 0.98 |
| 157_L | 276_Y | 1.308 | 0.98 |
| 132_V | 371_G | 1.298 | 0.98 |
| 6_A | 9_A | 1.283 | 0.97 |
| 288_V | 292_A | 1.278 | 0.97 |
| 227_L | 279_V | 1.274 | 0.97 |
| 58_V | 283_L | 1.271 | 0.97 |
| 145_V | 360_T | 1.271 | 0.97 |
| 355_E | 359_I | 1.270 | 0.97 |
| 54_C | 237_A | 1.265 | 0.97 |
| 121_I | 381_L | 1.260 | 0.97 |
| 50_F | 107_C | 1.258 | 0.97 |
| 375_A | 378_T | 1.246 | 0.97 |
| 62_Y | 95_Q | 1.245 | 0.97 |
| 351_L | 354_L | 1.242 | 0.97 |
| 179_L | 373_K | 1.230 | 0.96 |
| 55_I | 241_L | 1.228 | 0.96 |
| 55_I | 238_A | 1.228 | 0.96 |
| 246_G | 291_L | 1.219 | 0.96 |
| 366_V | 370_I | 1.211 | 0.96 |
| 145_V | 164_V | 1.205 | 0.96 |
| 375_A | 379_V | 1.202 | 0.96 |
| 285_I | 330_F | 1.194 | 0.96 |
| 15_T | 97_I | 1.192 | 0.96 |
| 66_F | 102_Q | 1.191 | 0.96 |
| 122_R | 125_A | 1.189 | 0.95 |
| 163_T | 167_I | 1.189 | 0.95 |
| 172_A | 368_A | 1.189 | 0.95 |
| 163_T | 360_T | 1.187 | 0.95 |
| 347_G | 351_L | 1.186 | 0.95 |
| 185_G | 191_F | 1.177 | 0.95 |
| 313_F | 317_G | 1.175 | 0.95 |
| 352_V | 355_E | 1.168 | 0.95 |
| 7_D | 92_S | 1.166 | 0.95 |
| 24_P | 201_T | 1.161 | 0.95 |
| 35_R | 119_E | 1.159 | 0.95 |
| 154_H | 352_V | 1.150 | 0.94 |
| 8_N | 94_Y | 1.150 | 0.94 |
| 93_I | 219_G | 1.141 | 0.94 |
| 234_V | 279_V | 1.138 | 0.94 |
| 38_N | 119_E | 1.130 | 0.94 |
| 114_V | 126_V | 1.118 | 0.93 |
| 296_G | 300_L | 1.116 | 0.93 |
| 317_G | 361_I | 1.114 | 0.93 |
| 39_V | 43_L | 1.113 | 0.93 |
| 175_V | 369_F | 1.112 | 0.93 |
| 135_T | 139_I | 1.105 | 0.93 |
| 242_G | 246_G | 1.101 | 0.92 |
| 4_D | 7_D | 1.097 | 0.92 |
| 167_I | 321_I | 1.096 | 0.92 |
| 7_D | 222_N | 1.094 | 0.92 |
| 16_A | 208_I | 1.090 | 0.92 |
| 228_A | 274_C | 1.089 | 0.92 |
| 278_G | 332_A | 1.088 | 0.92 |
| 16_A | 229_F | 1.088 | 0.92 |
| 210_W | 271_T | 1.087 | 0.92 |
| 151_L | 156_A | 1.076 | 0.91 |
| 261_S | 315_V | 1.070 | 0.91 |
| 17_L | 212_G | 1.069 | 0.91 |
| 242_G | 290_G | 1.065 | 0.91 |
| 236_T | 239_A | 1.063 | 0.91 |
| 361_I | 365_G | 1.063 | 0.91 |
| 166_H | 169_A | 1.061 | 0.90 |
| 285_I | 326_M | 1.059 | 0.90 |
| 48_V | 244_I | 1.056 | 0.90 |
| 284_I | 288_V | 1.055 | 0.90 |
| 28_L | 197_P | 1.051 | 0.90 |
| 108_I | 111_G | 1.049 | 0.90 |
| 141_I | 144_M | 1.047 | 0.90 |
| 178_Y | 306_V | 1.037 | 0.89 |
| 207_Y | 233_V | 1.036 | 0.89 |
| 218_A | 225_A | 1.035 | 0.89 |
| 171_I | 361_I | 1.034 | 0.89 |
| 134_L | 139_I | 1.029 | 0.89 |
| 56_L | 60_Y | 1.029 | 0.89 |
| 39_V | 194_H | 1.029 | 0.89 |
| 141_I | 363_W | 1.027 | 0.88 |
| 214_N | 271_T | 1.022 | 0.88 |
| 288_V | 326_M | 1.021 | 0.88 |
| 374_L | 377_L | 1.020 | 0.88 |
| 44_T | 123_F | 1.019 | 0.88 |
| 280_G | 284_I | 1.019 | 0.88 |
| 156_A | 324_C | 1.018 | 0.88 |
| 218_A | 222_N | 1.013 | 0.87 |
| 325_I | 357_I | 1.012 | 0.87 |
| 291_L | 295_W | 1.006 | 0.87 |
| 233_V | 236_T | 1.005 | 0.87 |
| 239_A | 262_G | 1.002 | 0.87 |
| 168_N | 364_S | 1.002 | 0.87 |
| 178_Y | 365_G | 1.001 | 0.87 |
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 | |
| 1u7gA | 1 | 0.9974 | 100 | 0.032 | Contact Map |
| 2b2hA | 1 | 0.9635 | 100 | 0.064 | Contact Map |
| 3b9wA | 1 | 0.8802 | 100 | 0.298 | Contact Map |
| 3hd6A | 1 | 0.9401 | 100 | 0.34 | Contact Map |
| 4m5bA | 1 | 0.4609 | 7 | 0.979 | Contact Map |
| 2qi9A | 2 | 0.4974 | 6.9 | 0.979 | Contact Map |
| 2mpnA | 2 | 0.1589 | 5.7 | 0.98 | Contact Map |
| 4d2bA | 1 | 0.4792 | 2.7 | 0.983 | Contact Map |
| 2xutA | 3 | 0.4375 | 2.4 | 0.983 | Contact Map |
| 4il6R | 1 | 0.0885 | 2.3 | 0.983 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)